Diff of the two buildlogs: -- --- b1/build.log 2024-11-29 12:02:13.981370951 +0000 +++ b2/build.log 2024-11-29 12:52:03.350252643 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 1 05:53:28 -12 2026 -I: pbuilder-time-stamp: 1767290008 +I: Current time: Sat Nov 30 02:02:20 +14 2024 +I: pbuilder-time-stamp: 1732881740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -37,54 +37,86 @@ dpkg-source: info: applying disable_inchi_test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/104417/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22658/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-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 Nov 29 12:02 /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/22658/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22658/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=22 ' - 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=10 ' + 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='ecc0c28ea03848d087f122a08d1803b1' - 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='104417' - PS1='# ' - PS2='> ' + INVOCATION_ID=44865c7e72b04a738013f4b79cc2ca0d + 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=22658 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.mBgU6r7Y/pbuilderrc_Lmbh --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.mBgU6r7Y/b1 --logfile b1/build.log rdkit_202409.2-2.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://213.165.73.152:3128' + 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.mBgU6r7Y/pbuilderrc_LZP7 --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.mBgU6r7Y/b2 --logfile b2/build.log rdkit_202409.2-2.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://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/104417/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/22658/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -572,7 +604,7 @@ Get: 367 http://deb.debian.org/debian unstable/main i386 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 368 http://deb.debian.org/debian unstable/main i386 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main i386 texlive-latex-extra all 2024.20241115-1 [24.6 MB] -Fetched 446 MB in 6s (68.9 MB/s) +Fetched 446 MB in 8s (53.8 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.) @@ -1760,8 +1792,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 1 17:54:28 UTC 2026. -Universal Time is now: Thu Jan 1 17:54:28 UTC 2026. +Local time is now: Fri Nov 29 12:03:53 UTC 2024. +Universal Time is now: Fri Nov 29 12:03:53 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:i386 (1.83.0-3.2+b1) ... @@ -2150,7 +2182,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202409.2/ && 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_202409.2-2_source.changes +I: user script /srv/workspace/pbuilder/22658/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/22658/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202409.2/ && 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_202409.2-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.2-2 dpkg-buildpackage: info: source distribution unstable @@ -2256,8 +2292,8 @@ -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/i386-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (2.0s) --- Generating done (1.2s) +-- Configuring done (4.6s) +-- Generating done (2.4s) CMake Warning: Manually-specified variables were not used by the project: @@ -2291,14 +2327,14 @@ -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/i386-linux-gnu/libpq.so (found version "17.2") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (0.5s) +-- Configuring done (1.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_build - cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -2315,9 +2351,9 @@ make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake "--color=" +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' @@ -2330,90 +2366,90 @@ cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build +make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202409.2/External/INCHI-API/python/inchi.py /build/reproducible-path/rdkit-202409.2/rdkit/Chem/inchi.py -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Leaving directory 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/RDGeneral/utils.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hc.c +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/GA/ga/BinaryStringChromosomePolicy.cpp +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/RDGeneral/versions.cpp +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/GA/util/RandomUtil.cpp +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/External/GA/util/Util.cpp +[ 1%] Linking CXX static library librdkitCatch.a +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu' -[ 1%] Built target hc +[ 1%] Built target rdkitCatch [ 2%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2024.09.2 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.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2024.09.2 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 2%] Built target ga -[ 2%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake -cd /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu' -[ 2%] Built target rdkitCatch [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.2 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 @@ -2432,178 +2468,150 @@ 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 -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Catalogs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Query /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Query /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -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/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 5%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 -[ 5%] Built target testMatCalc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testConcurrentQueue.dir/link.d CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 5%] Built target testConcurrentQueue -[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.2 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/SparseBitVect.cpp +[ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Query/test.cpp [ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 5%] Built target EigenSolvers -[ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so -cd /build/reproducible-path/rdkit-202409.2/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 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../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 5%] Built target SimDivPickers -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/SimDivPickers/testPickers.cpp +[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp +[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogParams.cpp +[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogEntry.cpp [ 5%] Linking CXX executable logTestsCatch cd /build/reproducible-path/rdkit-202409.2/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 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/DistPicker.cpp +[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.2 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Utils.cpp +[ 5%] Linking CXX executable testMatCalc +cd /build/reproducible-path/rdkit-202409.2/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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/MaxMinPicker.cpp In file included from /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap.cpp:17: /build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': /build/reproducible-path/rdkit-202409.2/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] @@ -2612,8 +2620,76 @@ /build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX executable dictTestsCatch +[ 5%] Linking CXX executable dictTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testDict.dir/link.d CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 5%] Built target testDict +[ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.2 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.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' @@ -2623,214 +2699,180 @@ 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/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.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[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make -f 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 7%] Built target dictTestsCatch -[ 7%] Linking CXX shared library ../../lib/libRDKitRDBoost.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2024.09.2 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 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object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoBitRanker.cpp +[ 8%] Linking CXX executable pickersTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/pickersTestsCatch.dir/link.d 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CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/LeaderPicker.cpp +In file included from /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 8%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +[ 8%] Built target rdMetricMatrixCalc +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 8%] Built target testFPB +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMultiFPB.dir/link.d CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 8%] Building CXX object 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/UniformGrid3D.cpp +[ 8%] Built target testMultiFPB +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD 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library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/InfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2024.09.2 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2024.09.2 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so -[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/wrap_FPB.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 9%] Built target InfoTheory +[ 8%] Built target InfoTheory make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make 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Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o +[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 9%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +In file included from /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: +/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here + 52 | return python::extract(dp_obj(i, j)); + | ^ +[ 8%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 9%] Built target RDGeometryLib +[ 8%] Built target RDGeometryLib make -f 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Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o +[ 8%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 9%] Built target pickersTestsCatch -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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.cpp /build/reproducible-path/rdkit-202409.2/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-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, @@ -2896,10 +2938,6 @@ /build/reproducible-path/rdkit-202409.2/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])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 9%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -[ 9%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /build/reproducible-path/rdkit-202409.2/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-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long long int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, @@ -3095,9 +3133,57 @@ /build/reproducible-path/rdkit-202409.2/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])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testFPB.dir/link.d CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2024.09.2 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+ 52 | return python::extract(dp_obj(i, j)); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]': +/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here + 52 | return python::extract(dp_obj(i, j)); + | ^ +[ 9%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 +[ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 9%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 9%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 9%] Built target ChemicalFeatures +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Atom.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 9%] Built target testFPB +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 9%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.cpp make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" @@ -3106,17 +3192,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 9%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/testTransforms.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMultiFPB.dir/link.d CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 9%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 9%] Built target testMultiFPB +[ 9%] Built target cQuantize make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Geometry/testGrid.cpp +[ 9%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdSimDivPickers.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKithc.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 9%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" @@ -3133,13 +3218,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 9%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Geometry/catch_tests.cpp -[ 10%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/wrap_BitOps.cpp +[ 10%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2024.09.2 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 10%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 -[ 10%] Built target testDataStructs +[ 10%] Built target Alignment make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" @@ -3148,10 +3234,34 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 10%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Geometry/Wrap/Point.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/ChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2024.09.2 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2024.09.2 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so +In file included from /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap/RDBase.cpp:14: +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +[ 10%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +[ 10%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 10%] Built target ChemicalFeatures +[ 10%] Built target rdInfoTheory make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" @@ -3160,44 +3270,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 11%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Numerics/testConrec.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: -/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here - 52 | return python::extract(dp_obj(i, j)); - | ^ -[ 11%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -[ 11%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 11%] Built target rdMetricMatrixCalc -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake "--color=" -[ 11%] Built target Clustering -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/QueryAtom.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build -[ 11%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Geometry/Wrap/UniformGrid3D.cpp -[ 11%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryBond.cpp -[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2024.09.2 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testTransforms.dir/link.d CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 11%] Built target Alignment +[ 11%] Built target testTransforms 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" @@ -3206,96 +3281,121 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 11%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/Numerics/Alignment/testAlignment.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Bond.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/LeaderPicker.cpp:19: -In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)', - inlined from 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]' at /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/LeaderPicker.h:263:18: -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]': -/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here - 52 | return python::extract(dp_obj(i, j)); - | ^ -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolOps.cpp -[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 -[ 12%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 +[ 11%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGrid.dir/link.d CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +In file included from /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:18: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long int]': +/build/reproducible-path/rdkit-202409.2/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] + 68 | T res = python::extract(d_seq[which]); + | ^~~ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long unsigned int]': +/build/reproducible-path/rdkit-202409.2/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]); + | ^~~ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 13%] Built target rdSimDivPickers -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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testConrec -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolPickler.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Canon.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD 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../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 14%] Built target rdGeometry [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/AtomIterators.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o @@ -3308,66 +3408,28 @@ cd 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-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-202409.2/Code/GraphMol/ConjugHybrid.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/AddHs.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Matrices.cpp +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 147 | numNonCandRings < numAtomRings) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Chirality.cpp -[ 14%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 14%] Built target rdAlignment [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RingInfo.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:18: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long int]': -/build/reproducible-path/rdkit-202409.2/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] - 68 | T res = python::extract(d_seq[which]); - | ^~~ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Conformer.cpp -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long unsigned int]': -/build/reproducible-path/rdkit-202409.2/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]); - | ^~~ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Renumber.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/AdjustQuery.cpp -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 147 | numNonCandRings < numAtomRings) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StereoGroup.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/new_canon.cpp -[ 15%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 15%] Built target rdGeometry [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SubstanceGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o @@ -3382,32 +3444,6 @@ cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/WedgeBonds.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProps.cpp -[ 16%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 16%] Built target cDataStructs -In file included from /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap/RDBase.cpp:14: -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ [ 16%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2024.09.2 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/Atropisomers.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o CMakeFiles/GraphMol.dir/MolProps.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3423,67 +3459,44 @@ 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/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd 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Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 20%] Linking CXX executable tableTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/Subgraphs.cpp +[ 17%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Parser.cpp +[ 17%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 23%] Built target MolTransforms -[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/sln.tab.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 23%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now 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Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/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-202409.2/Code/GraphMol/Wrap/Queries.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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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shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +[ 20%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Node.cpp +[ 23%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 24%] Built target rdPartialCharges -[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SLNParse/lex.yysln.cpp +[ 23%] Built target rdtrajectory make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend +[ 23%] Built target rdBase +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make 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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-202409.2/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 24%] Built target SubstructMatch +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.cpp -[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraint.cpp -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.cpp -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o +[ 24%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 24%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +[ 24%] Built target ShapeHelpers +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o cd 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../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 24%] Built target rdMolTransforms +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd 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26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 27%] Built target SLNParse -[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +[ 26%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/BondStretch.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E 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cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.2 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.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.2 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 27%] Built target ShapeHelpers -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend +[ 26%] Built target SLNParse +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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 28%] Built target rdqueries -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 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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-202409.2/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 28%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +/usr/bin/c++ -fPIC -g -O2 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CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.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/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 28%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +[ 28%] Built target ForceField +[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 28%] Built target rdSLNParse +[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -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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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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build +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-202409.2/obj-i686-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 28%] Built target rdCIPLabeler [ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 28%] 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 -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/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 -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend -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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 29%] Built target rdSLNParse -[ 29%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 -[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 29%] Built target queryTestsCatch +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-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 29%] Built target rdCIPLabeler -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/test2.cpp +[ 29%] Linking CXX executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 +[ 29%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && 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/usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 29%] Built target SubstructMatch -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend +[ 29%] Built target graphmolcpTest +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +[ 29%] Built target moliteratorTestsCatch +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Filters.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 30%] Built target molbundleTestsCatch +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make 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-c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Filters.cpp -[ 30%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.2 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 31%] Linking CXX executable v2smiTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +[ 31%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code 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CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp -[ 30%] Linking CXX executable subgraphsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/subgraphsCatch.dir/link.txt --verbose=1 -[ 30%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 32%] Linking CXX executable v2smiTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 31%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 31%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 +[ 32%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -[ 32%] Linking CXX executable moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 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CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so +[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MACCS.cpp +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 36%] Built target ForceFieldHelpers +[ 35%] Built target Abbreviations make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/catch_tests.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 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.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +[ 35%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 35%] Built target MolChemicalFeatures make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom 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Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 35%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistGeomUtils.cpp +[ 35%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 35%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp -[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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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object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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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-202409.2/Code/GraphMol/Depictor/Templates.cpp +[ 35%] Linking CXX executable forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +[ 35%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 36%] Built target ForceFieldsCatch -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +[ 35%] Built target rdCoordGen +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem 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../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 37%] Built target Depictor +[ 36%] Built target Depictor make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend -make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake 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External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContrib.cpp +[ 37%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +[ 37%] Built target rdForceField +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms 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CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -[ 39%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.2 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o 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Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/testDistGeom.cpp +[ 37%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 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.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd 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Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +[ 37%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolHash/normalize.cpp +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-202409.2/obj-i686-linux-gnu' -cd 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 38%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && 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Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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-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-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.2 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 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/usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 40%] Built target Fingerprints +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 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Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +[ 40%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-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-202409.2/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 40%] Built target MolHash +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 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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 -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 40%] Linking CXX executable smaTest1 make 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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 -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -/usr/bin/c++ -g 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target smaTest1 -[ 40%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +[ 41%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 40%] Built target DistGeom -[ 40%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2024.09.2 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/i386-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.2 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 40%] 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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" +[ 41%] Built target DistGeom +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolChemicalFeatures.dir/link.d -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.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 41%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/External/INCHI-API/Wrap/pyInchi.cpp -[ 41%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 +[ 41%] Built target rdMolChemicalFeatures +[ 41%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 41%] Built target rdBase -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 41%] Built target rdinchi +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 41%] Built target rdDepictor +[ 41%] Built target rdMolHash [ 42%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4607,11 +4653,6 @@ /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 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Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/ChemTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4624,62 +4665,67 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o [ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o [ 43%] Building 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SDWriter.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/XYZFileParser.cpp [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 45%] Built target rdfiltercatalog [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o @@ -4696,16 +4742,6 @@ cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 45%] Built target rdFingerprintGenerator -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o 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rdfiltercatalog [ 46%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 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/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.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4714,198 +4750,258 @@ [ 46%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 46%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/testMMFFForceField.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/molopstest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/testChirality.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/testPicklerGlobalSettings.cpp +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/resMolSupplierTest.cpp +[ 49%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 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graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 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+[ 49%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_adjustquery.cpp +[ 49%] Linking CXX executable graphmolOrganometallicsCatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -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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graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 49%] Built 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 49%] Built target test-valgrind +[ 49%] Built target graphmolSGroupCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 49%] Built target graphmolOrganometallicsCatch +[ 49%] Built target graphmoltestChirality make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp -[ 50%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 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/usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MDLParser.cpp -[ 50%] Built target resMolSupplierTest +[ 50%] Built target graphmolAdjustQueryCatch 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/pickleTestsCatch.dir/link.d 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nontetrahedralCatch.dir/link.d CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target testUFFForceField +[ 50%] Built target nontetrahedralCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" @@ -4968,11 +5064,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testAtropisomers.cpp -[ 50%] Linking CXX executable molBundleTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molBundleTest.dir/link.d CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/DaylightParser.cpp +[ 50%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target molBundleTest +[ 50%] Built target testAtropisomers make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" @@ -4981,85 +5079,82 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp -[ 50%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target graphmoltestPicklerGlobalSetting -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 50%] Linking CXX executable graphmolAdjustQueryCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 50%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202409.2/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 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+cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 50%] Linking CXX executable testSquiggleDoubleBonds +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 50%] Built target testSquiggleDoubleBonds +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testMolSupplier.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testGeneralFileReader.cpp -[ 50%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable graphmolTestsCatch +[ 50%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target graphmolSGroupCatch +[ 50%] Built target depictorCatch 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 50%] Built target testGeneralFileReader 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testTpls.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testMolWriter.cpp +[ 50%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +[ 50%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 50%] Built target smiTest1 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" @@ -5068,6 +5163,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testMol2ToMol.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 50%] Built target smiTestCatch 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" @@ -5076,11 +5174,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testSequence.cpp -[ 50%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target testAtropisomers +[ 50%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -5089,11 +5187,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 50%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 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../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 50%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target testMultithreadedMolSupplier -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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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/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testPropertyLists.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 +[ 50%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target testGeneralFileReader +[ 50%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" @@ -5139,16 +5228,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 50%] Built target testSequence [ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -[ 51%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Built target testMol2ToMol +[ 51%] Built target testMolSupplier 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" @@ -5170,11 +5256,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 51%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Built target testTplParser +[ 51%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" @@ -5183,105 +5269,106 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 52%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 52%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MoleculeParser.cpp -[ 51%] Linking CXX executable XYZFileParserCatchTest +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 52%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -[ 51%] Linking CXX executable connectTheDotsTest +[ 52%] Linking CXX executable connectTheDotsTest cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Built target connectTheDotsTest +[ 52%] Built target XYZFileParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Built target XYZFileParserCatchTest +[ 52%] Built target connectTheDotsTest make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp -[ 51%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 51%] Built target graphmoltestPickler -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 52%] Built target molfileStereoCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 52%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -[ 52%] Linking CXX executable molfileStereoCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 52%] Built target molfileStereoCatchTest +[ 53%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/catch_tests.cpp +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 53%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 52%] Linking CXX executable v2MolSuppliers -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o +[ 53%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 53%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target testMolWriter +[ 53%] Built target testPropertyLists make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -5290,11 +5377,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 53%] Linking CXX executable v2FileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target v2FileParsersCatchTest +[ 53%] Built target multithreadedSupplierCatchTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" @@ -5303,6 +5390,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/test1.cpp +[ 53%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { @@ -5334,41 +5425,37 @@ /build/reproducible-path/rdkit-202409.2/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)}) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 53%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target smiTest1 +[ 53%] Built target testFragCatalog 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake "--color=" @@ -5377,45 +5464,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/test1.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target depictorCatch +[ 53%] Built target substructTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" -[ 53%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target testMMFFForceField -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 53%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target filterCatalogTest -[ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp -[ 53%] Linking CXX executable graphmolTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/graphmolTest1.dir/link.d CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target graphmolTest1 -[ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 53%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 53%] Built target testFragCatalog +[ 53%] Built target testSubstructMatch 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5426,227 +5492,190 @@ cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp -[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors.cpp -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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" -[ 54%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Fingerprints/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/CDXMLParser.cpp -[ 55%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -[ 55%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=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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(i < count) && (k < horz); k++) { - | ~~^~~~~~~ -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 58%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +[ 57%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 57%] Built target testFingerprints 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 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../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=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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../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 58%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -[ 58%] Built target graphmolTestsCatch +[ 57%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +[ 58%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 59%] Built target testSubstructMatch +[ 58%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o +[ 58%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testMolAlign.cpp 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-202409.2/obj-i686-linux-gnu' @@ -5654,80 +5683,109 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o +[ 58%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/catch_tests.cpp +[ 58%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +[ 58%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +[ 59%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 59%] Built target testShapeHelpers +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +[ 59%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script 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-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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/FMCS.cpp -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': -/build/reproducible-path/rdkit-202409.2/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) { - | ~~^~~~~~~~~~ +[ 60%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +[ 60%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 60%] Built target testMolAlign make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 62%] Built target testCrystalForceField +[ 61%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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-Wl,--dependency-file,CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 62%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd /build/reproducible-path/rdkit-202409.2/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 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../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so +[ 62%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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/usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Built target testMolCatalog -[ 64%] Built target molAlignCatchTest -[ 64%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Built target testFingerprintGenerators +[ 63%] Built target distGeomHelpersCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 63%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Seed.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 64%] Built target testDistGeomHelpers make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" @@ -5803,11 +5866,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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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Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 64%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd 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../../../lib/libRDKitSubgraphs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2024.09.2 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Built target testMolAlign +[ 64%] Built target Deprotect 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" @@ -5816,11 +5880,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rdmolops.cpp -[ 64%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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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/build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Built target testFeatures +[ 64%] Built target molHashCatchTest make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" @@ -5829,10 +5895,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/catch_tests.cpp -[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Seed.cpp -[ 64%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 [ 64%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -5841,195 +5903,368 @@ make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 64%] Built target molHashCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build -[ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolOps.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 64%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o cd 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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/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -MF CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o.d -o CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/MolProcessing.cpp -[ 64%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -[ 64%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2024.09.2 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.2 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so +[ 64%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o +[ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_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/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/EEM.cpp +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolOps.cpp:36: +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +[ 66%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinWriter.cpp +[ 67%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +[ 68%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2024.09.2 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 65%] Built target distGeomHelpersCatch +[ 68%] Built target FMCS make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make 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object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +[ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/catch_tests.cpp -[ 65%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -[ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 65%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.2 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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-202409.2/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 68%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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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/usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 65%] Built target molInterchangeTest1 +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/WHIM.cpp +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': +/build/reproducible-path/rdkit-202409.2/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) { + | ~~^~~~~~~~~~ +[ 71%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 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Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp +[ 71%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 71%] Built target MarvinParser 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +[ 71%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 65%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 71%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Charge.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdmolops.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 71%] Built target rdmolops +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 71%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': +/build/reproducible-path/rdkit-202409.2/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, + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 65%] Built target molInterchangeCatchTest +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +[ 71%] Built target rxnTestCatch +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +[ 71%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 66%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 66%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 -[ 66%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testAbbreviations.dir/link.d CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 66%] Built target testAbbreviations -[ 66%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 67%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Built target MolProcessing -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 67%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +[ 71%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202409.2/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 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../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Built target testReactionFingerprints -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend +[ 71%] Built target Descriptors +make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Deprotect.cpp -[ 67%] Linking CXX executable testMMPA +[ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Built target testMMPA -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/processing_tests.cpp -[ 67%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp +[ 71%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Built target testEnumeration -make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend +[ 71%] Built target FMCStest +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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp +[ 71%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.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, @@ -6052,88 +6287,57 @@ /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 67%] Built target rdMMPA -[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -cd 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../../../lib/libRDKitDeprotect.so.1.2024.09.2 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 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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/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinDefs.cpp -[ 70%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +[ 71%] Built target rdMMPA +make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 70%] Built target testDistGeomHelpers -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolDraw2D/DrawShape.cpp -[ 70%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -[ 70%] Linking CXX executable testMolProcessing -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 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.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && 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object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-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-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 70%] Built target MolEnumerator +[ 72%] Built target rdFMCS make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" -[ 70%] Built target testMolProcessing -make -f 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CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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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-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +[ 74%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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74%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202409.2/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdDeprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 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object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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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-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +[ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 76%] Built target rdMolEnumerator +make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse 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+cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 79%] Linking CXX executable testMrvToMol +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.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/libRDKitMarvinParser.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 80%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 /usr/lib/libCatch2.a 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 80%] Built target testGenericGroups +[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_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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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testAUTOCORR2D.dir/link.d CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o cd 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 81%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 73%] Built target rdMolEnumerator +[ 81%] Built target TautomerQuery make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors 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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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testEEM.cpp -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -[ 73%] Linking CXX executable testATF +[ 81%] Linking CXX executable testATF cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testATF.dir/link.d CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 73%] Built target testATF +[ 81%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testPBF.cpp +[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SDMolSupplier.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-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here + 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MaeMolSupplier.cpp:23: +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MaeWriter.cpp:21: +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 81%] Linking CXX executable testBCUT +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/TDTMolSupplier.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 81%] Built target testBCUT make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 85%] Linking CXX executable testGETAWAY +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SmilesWriter.cpp:20: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 78%] Built target testMORSE +[ 85%] Built target testGETAWAY make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +[ 85%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 78%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 85%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 78%] Built target testRDFcustom +[ 85%] Built target testCoulombMat make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolDraw2D/test1.cpp -[ 78%] Linking CXX executable testGETAWAY -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 86%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 78%] Built target testGETAWAY +[ 86%] Built target testAUTOCORR3D 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' 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-202409.2/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 78%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/PDBWriter.cpp +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SDWriter.cpp:21: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTWriter.cpp:21: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp +/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Mol.cpp +[ 87%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 87%] Built target descriptorsTestCatch 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 79%] Built target testAUTOCORR3D -[ 79%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so 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/build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2024.09.2 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.2 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target RascalMCES -make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend -make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend -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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -[ 80%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -[ 80%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/mces_catch.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 80%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target testCoulombMat -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': -/build/reproducible-path/rdkit-202409.2/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, - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -[ 80%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 -[ 80%] Linking CXX executable testDescriptors -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testDescriptors.dir/link.d CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target testDescriptors -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolOps.cpp:36: +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Conformer.cpp +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/reproducible-path/rdkit-202409.2/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-202409.2/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())); @@ -6629,428 +7130,492 @@ /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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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.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 88%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] 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 -[ 80%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +[ 88%] Built target O3AAlign +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/RingInfo.cpp +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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/freetype2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp: In function 'void RDKit::SetPos(Conformer*, const boost::python::numpy::ndarray&)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp:72:22: warning: comparison of integer expressions of different signedness: 'Py_intptr_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 72 | if (array.shape(0) != conf->getNumAtoms()) { + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 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/usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 88%] Built target rdmolfiles +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MonomerInfo.cpp +In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp:21: +/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MolBundle.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/StereoGroup.cpp +[ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: note: '' declared here + 77 | double r = python::extract(tDict.values()[i]); + | ^ +[ 88%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 88%] Built target GeneralizedSubstruct +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Chirality.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-202409.2/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-202409.2/Code/GraphMol/Wrap/StereoGroup.cpp:36:22: +/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/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/test1.cpp +[ 88%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/moldraw2DTest1.dir/link.d 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 88%] Built target moldraw2DTest1 +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize 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-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-202409.2/Code/GraphMol/MolStandardize/testCharge.cpp +[ 88%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/testValidate.cpp -[ 80%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -[ 80%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target descriptorsTestCatch +[ 88%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 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../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 80%] Built target moldraw2DRxnTest1 +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-202409.2/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-202409.2/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-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:72: note: '' declared here + 65 | unsigned int sz = python::extract(pts.attr("__len__")()); + | ^ +[ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 88%] Built target rdMolDescriptors make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/test2.cpp -[ 80%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 88%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target testMolEnumerator +[ 88%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/testFragment.cpp -[ 80%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -[ 80%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +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())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.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-202409.2/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-202409.2/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 80%] Built target O3AAlign +[ 88%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/catch_tests.cpp -[ 80%] Built target testRascalCluster +[ 88%] Linking CXX executable molChargeTest +cd 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testPipeline.cpp -[ 81%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 81%] Built target FMCStest +[ 89%] Built target molStandardizeSmallTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 81%] Built target molNormalizeTest -[ 82%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 82%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 82%] Built target molStandardizeSmallTest -[ 82%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Charge.cpp -[ 82%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 82%] Built target molChargeTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +[ 89%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -[ 82%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 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-DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp -[ 82%] Linking CXX executable molFragmentTest +[ 89%] Linking CXX executable molFragmentTest cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so -cd /build/reproducible-path/rdkit-202409.2/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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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../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 82%] Built target molFragmentTest -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +[ 89%] Built target molFragmentTest +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd 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CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp +[ 89%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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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Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 82%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -[ 82%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -[ 83%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 83%] Built target molStandardizeTest -[ 83%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB 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-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so -[ 83%] Built target MarvinParser -[ 83%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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-202409.2/Code/GraphMol/MolStandardize/Wrap/Metal.cpp -[ 83%] Built target TautomerQuery -[ 83%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 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Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: note: '' declared here - 77 | double r = python::extract(tDict.values()[i]); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:460:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 460 | (python::len(prbCrippenContribs) == prbNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:475:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 475 | (python::len(refCrippenContribs) == refNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:536:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 536 | (python::len(prbCrippenContribs) == prbNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:551:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 551 | (python::len(refCrippenContribs) == refNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 84%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +[ 90%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB 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Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp +[ 90%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.2 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.2 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Built target ScaffoldNetwork -make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 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object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp +[ 91%] Linking CXX executable molStandardizePipelineTest cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 91%] Built target rdMolDraw2D +[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp +/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': +/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1617:38: warning: unused parameter 'data' [-Wunused-parameter] + 1617 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~~~^~~~ +/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1617:49: warning: unused parameter 'isQuery' [-Wunused-parameter] + 1617 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1618:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] + 1618 | unsigned int bitFlags) { + | ~~~~~~~~~~~~~^~~~~~~~ +[ 92%] Linking CXX executable generalizedSubstructCatch +cd 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/usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Built target testO3AAlign +[ 93%] Built target molStandardizeCatchTest 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-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +[ 93%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp -[ 84%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdchem.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Built target molTautomerTest -make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" +[ 93%] Built target rdchem +[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp +[ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/catch_tests.cpp -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend +[ 93%] Built target rdGeneralizedSubstruct +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp -[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -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-202409.2/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-202409.2/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-202409.2/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-202409.2/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:54: note: '' declared here - 218 | return python::extract(dp_obj(boost::ref(m))); - | ^ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 84%] Built target rdMolAlign -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend +[ 93%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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 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-I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_op.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/cache.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/guc.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/low_gist.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/mol_op.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rdkit_gist.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gist.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_gin.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bitstring.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rdkit_io.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rxn_op.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o +cd 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CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rdmolfiles.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/data +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 86%] Built target testGenericGroups +[ 95%] Built target tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/expected make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu 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/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o 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../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 86%] Built target testMrvToMol -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 95%] Built target rdkit +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-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:15: /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202409.2/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] @@ -7065,6 +7630,20 @@ /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:460:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 460 | (python::len(prbCrippenContribs) == prbNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:475:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 475 | (python::len(refCrippenContribs) == refNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:536:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 536 | (python::len(prbCrippenContribs) == prbNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:551:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 551 | (python::len(refCrippenContribs) == refNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202409.2/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-202409.2/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())); @@ -7072,574 +7651,87 @@ /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -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-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here - 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp +[ 96%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 87%] Built target rdTautomerQuery -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MaeWriter.cpp -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SDMolSupplier.cpp -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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here - 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 87%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 87%] Built target moldraw2DTest1 -[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/CIPLabeler/Node.cpp -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 87%] Built target GeneralizedSubstruct -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 87%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Table.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 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../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 87%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -[ 87%] Built target rdMolStandardize -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Atom.cpp -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Bond.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdmolops.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 87%] Built target rdmolops -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SmilesWriter.cpp -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-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 88%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MaeMolSupplier.cpp:23: -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MaeWriter.cpp:21: -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -[ 88%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Edge.cpp -[ 88%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 88%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Mol.cpp -[ 89%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -[ 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../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make 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Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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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-202409.2/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 96%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o 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../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/RGroupData.cpp -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Conformer.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SmilesWriter.cpp:20: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp -[ 91%] Building 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-O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" +[ 96%] Built target RGroupDecomposition +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E 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/usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build +[ 96%] Built target rdMolAlign +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-202409.2/obj-i686-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp: In function 'void RDKit::SetPos(Conformer*, const boost::python::numpy::ndarray&)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp:72:22: warning: comparison of integer expressions of different signedness: 'Py_intptr_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 72 | if (array.shape(0) != conf->getNumAtoms()) { - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 92%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 92%] Built target rdMolDraw2D -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SDWriter.cpp:21: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build +[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK 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+cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql 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-I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/rxn_op.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -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 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sfp_op.c -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp [ 96%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 96%] Built target testScaffoldNetwork -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/Wrap/Chirality.cpp -[ 96%] Linking CXX executable generalizedSubstructCatch -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Conformer.cpp:21: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 96%] Built target generalizedSubstructCatch -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-202409.2/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-202409.2/Code/GraphMol/Wrap/StereoGroup.cpp:36:22: -/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())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX shared library librdkit.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/sql -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/data -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit/expected -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/lib /usr/lib/i386-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 96%] Built target rdkit -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/PDBWriter.cpp:20: -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -In file included from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTWriter.cpp:21: -/build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202409.2/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-202409.2/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-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -[ 96%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 96%] Built target RGroupDecomposition -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition 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Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/depend -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o [ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/GaExample.cpp -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp In file included from /usr/include/boost/python/override.hpp:13, @@ -7647,81 +7739,25 @@ 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-202409.2/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-202409.2/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] + 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-202409.2/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-202409.2/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-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:72: note: '' declared here - 65 | unsigned int sz = python::extract(pts.attr("__len__")()); - | ^ +/build/reproducible-path/rdkit-202409.2/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-202409.2/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:54: note: '' declared here + 218 | return python::extract(dp_obj(boost::ref(m))); + | ^ [ 97%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 97%] Built target gaExample /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 97%] Built target testRGroupDecompInternals -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 executable testReaction -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 97%] 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_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-202409.2/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-202409.2/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())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdChemReactions.dir/link.d -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.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 97%] Built target rdChemReactions [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so @@ -7730,30 +7766,40 @@ [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' 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-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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-202409.2/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdMolStandardize.dir/link.d -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 CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 99%] Built target rdMolStandardize +[ 99%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 99%] Built target gaExample [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7764,16 +7810,6 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitga.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' [ 99%] Built target rdRGroupDecomposition -[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdmolfiles.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 99%] Built target rdmolfiles -[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdchem.dir/link.d -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.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[ 99%] Built target rdchem [ 99%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7810,16 +7846,16 @@ /build/reproducible-path/rdkit-202409.2/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so +cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdSubstructLibrary.dir/link.d -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.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' +[ 99%] Built target rdSubstructLibrary [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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 -Wl,--dependency-file,CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/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-202409.2=. -fstack-protector-strong -Wformat -Werror=format-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,--dependency-file,CMakeFiles/rdSubstructLibrary.dir/link.d -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.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -[100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' @@ -7949,73 +7985,73 @@ Searching for files to exclude Searching 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for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DetermineBonds -Searching for files in directory 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directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DetermineBonds +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers +Searching for files in directory 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for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StructChecker +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/libs +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc @@ -8029,9 +8065,9 @@ Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures @@ -9020,15 +9056,15 @@ Generating code for file FourthDimContribs.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... +Generating code for file AngleConstraint.h... +Generating code for file AngleConstraint.h... +Generating code for file AngleConstraint.h... Generating code for file AngleConstraints.h... Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... -Generating code for file AngleConstraint.h... -Generating code for file AngleConstraint.h... -Generating code for file AngleConstraint.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file Contribs.h... @@ -9285,6 +9321,8 @@ Generating code for file MolStandardize.h... Generating code for file Normalize.h... Generating code for file Pipeline.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... @@ -9346,8 +9384,6 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... -Generating code for file Tautomer.h... -Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -9454,15 +9490,15 @@ Generating docs for file FourthDimContribs.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... +Generating docs for file AngleConstraint.h... +Generating docs for file AngleConstraint.h... +Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraints.h... Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... -Generating docs for file AngleConstraint.h... -Generating docs for file AngleConstraint.h... -Generating docs for file AngleConstraint.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file Contribs.h... @@ -9721,6 +9757,8 @@ Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... Generating docs for file Pipeline.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... @@ -9782,8 +9820,6 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... -Generating docs for file Tautomer.h... -Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -13083,7 +13119,7 @@ done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book Cookbook Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.rdMolDraw2DQt source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.RegistrationHash source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.SpacialScore source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.Chem.rdMolEnumerator source/rdkit.Chem.rdCIPLabeler source/rdkit.Chem.rdTautomerQuery source/rdkit.Chem.rdEHTTools source/rdkit.Chem.rdDetermineBonds source/rdkit.Chem.rdShapeAlign source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.cQuantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.MatOps source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemutils source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner GettingStartedInC++ resolving references... -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -16107,10 +16143,10 @@ find /build/reproducible-path/rdkit-202409.2 -name rdchem.so /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/:/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" dh_auto_test - cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 + cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j22 +/usr/bin/ctest --force-new-ctest-process --verbose -j10 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -16183,6 +16219,121 @@ 10: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 +3: [02:43:31] Testing Github940: property dictionaries leaking memory +3: [02:43:31] done +3: Testing RDValue +3: Testing RDAny +3: dict set int vect +3: dict get int vect +4: -- running tests -- +4: min: -2147483648 -2147483648 +4: min: 0 0 +4: min: 2.22507e-308 2.22507e-308 +4: min: 1.17549e-38 1.17549e-38 +4: min: 0 0 +4: == int +4: == double +4: == float +4: == unsigned int +4: == bool +4: == std::string +5: [02:43:31] +5: ----------------------------------------- +5: [02:43:31] Finished: testPushAndPop() +5: [02:43:31] +5: ----------------------------------------- +5: [02:43:31] +5: ----------------------------------------- +6: Randomness seeded to: 678543797 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: Randomness seeded to: 87097876 +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: [02:43:31] should not be silent +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: +8: [02:43:31] pass +8: [02:43:31] v3 4 +8: [02:43:31] v4 5 +8: [02:43:31] SPARSE ----------------------------------- +8: [02:43:31] Set 10: 0 +8: [02:43:31] Set 11: 0 +8: [02:43:31] Set 14: 0 +8: [02:43:31] Set 10: 1 +8: [02:43:31] Get 14: 1 +8: [02:43:31] Num: 20 +8: [02:43:31] NumOn: 3 +8: [02:43:31] NumOff: 17 +8: 10, 11, 14, +8: [02:43:31] t2[19]: 0 +8: [02:43:31] t2[14]: 1 +8: [02:43:31] t2[19]: 0 +8: [02:43:31] t2[14]: 0 +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +8: t1^t2: 14, 15, 17, +8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +8: except +8: [02:43:31] Explicit ---------------------------------- +8: [02:43:31] Set 10: 0 +8: [02:43:31] Set 11: 0 +8: [02:43:31] Set 14: 0 +8: [02:43:31] Set 10: 1 +8: [02:43:31] Get 14: 1 +8: [02:43:31] Num: 20 +8: [02:43:31] NumOn: 3 +8: [02:43:31] NumOff: 17 +8: 10, 11, 14, +8: [02:43:31] t2[19]: 0 +8: [02:43:31] t2[14]: 1 +8: [02:43:31] t2[19]: 0 +8: [02:43:31] t2[14]: 0 +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +8: t1^t2: 14, 15, 17, +8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +8: except +8: [02:43:31] Done +8: [02:43:31] Test DiscreteValue Vectors 1 ---------------------------- +8: [02:43:31] Expected failure: Value out of range +8: [02:43:31] Expected failure: Value out of range +8: [02:43:31] Expected failure: Value out of range +8: [02:43:31] Expected failure: Value out of range +8: [02:43:31] Expected failure: Value out of range +8: [02:43:31] Test DiscreteValue Vectors 2 ------------------------------ +8: [02:43:31] Test DiscreteValue Vectors 3 --------------------------- +8: [02:43:31] Test DiscreteValue Operations ----------------------------- +8: [02:43:31] Test DiscreteValue Operations 2 -------------------------- +8: [02:43:31] Test SparseIntVect ------------------------------------ +8: [02:43:31] Test SparseIntVect Serialization -------------------------- +8: [02:43:31] Test BitVect Serialization ------------------------------- +8: [02:43:31] Test BitVect to FPS ------------------------------- +8: [02:43:31] Test BitVect to binary string ------------------------------- +8: [02:43:31] Test Similarity Measures BitVect ------------------------------- +8: [02:43:31] Test Similarity Measures SparseBitVect ------------------------------- +8: [02:43:31] Test BitVect with all ones ------------------------------- +8: [02:43:31] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [02:43:31] Test bitmap operations ------------------------------- +8: [02:43:31] Test bitmaps as properties ------------------------------- +8: [02:43:31] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- + 1/230 Test #4: testRDValue ............................ Passed 0.06 sec + 2/230 Test #6: dictTestsCatch ......................... Passed 0.05 sec + 3/230 Test #7: logTestsCatch .......................... Passed 0.05 sec + 4/230 Test #9: testFPB ................................ Passed 0.04 sec test 11 Start 11: catchDataStructs @@ -16207,6 +16358,13 @@ 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testSparseIntVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 + 5/230 Test #8: testDataStructs ........................ Passed 0.07 sec +11: Randomness seeded to: 174799607 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 6/230 Test #10: testMultiFPB ........................... Passed 0.06 sec + 7/230 Test #11: catchDataStructs ....................... Passed 0.03 sec test 15 Start 15: pyFPB @@ -16225,36 +16383,6 @@ 17: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/testGrid 17: Working Directory: /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch -18: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry -18: Test timeout computed to be: 1500 -test 19 - Start 19: testPyGeometry - -19: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/testGeometry.py" -19: Working Directory: /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu/Code/Numerics/testMatrices -20: Working Directory: /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu/Code/Numerics/testConrec -21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics -21: Test timeout computed to be: 1500 -test 22 - Start 22: testAlignment - -22: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment -22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment -22: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -16365,229 +16493,6 @@ 1: 12 1 1 0 1: M END 1: -3: [06:21:43] Testing Github940: property dictionaries leaking memory -3: [06:21:43] done -3: Testing RDValue -3: Testing RDAny -3: dict set int vect -3: dict get int vect -4: -- running tests -- -4: min: -2147483648 -2147483648 -4: min: 0 0 -4: min: 2.22507e-308 2.22507e-308 -4: min: 1.17549e-38 1.17549e-38 -4: min: 0 0 -4: == int -4: == double -4: == float -4: == unsigned int -4: == bool -4: == std::string -5: [06:21:43] -5: ----------------------------------------- -5: [06:21:43] Finished: testPushAndPop() -5: [06:21:43] -5: ----------------------------------------- -5: [06:21:43] -5: ----------------------------------------- -6: Randomness seeded to: 1493203401 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: Randomness seeded to: 828116074 -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: [06:21:43] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: -8: [06:21:43] pass -8: [06:21:43] v3 4 -8: [06:21:43] v4 5 -8: [06:21:43] SPARSE ----------------------------------- -8: [06:21:43] Set 10: 0 -8: [06:21:43] Set 11: 0 -8: [06:21:43] Set 14: 0 -8: [06:21:43] Set 10: 1 -8: [06:21:43] Get 14: 1 -8: [06:21:43] Num: 20 -8: [06:21:43] NumOn: 3 -8: [06:21:43] NumOff: 17 -8: 10, 11, 14, -8: [06:21:43] t2[19]: 0 -8: [06:21:43] t2[14]: 1 -8: [06:21:43] t2[19]: 0 -8: [06:21:43] t2[14]: 0 -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -8: t1^t2: 14, 15, 17, -8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -8: except -8: [06:21:43] Explicit ---------------------------------- -8: [06:21:43] Set 10: 0 -8: [06:21:43] Set 11: 0 -8: [06:21:43] Set 14: 0 -8: [06:21:43] Set 10: 1 -8: [06:21:43] Get 14: 1 -8: [06:21:43] Num: 20 -8: [06:21:43] NumOn: 3 -8: [06:21:43] NumOff: 17 -8: 10, 11, 14, -8: [06:21:43] t2[19]: 0 -8: [06:21:43] t2[14]: 1 -8: [06:21:43] t2[19]: 0 -8: [06:21:43] t2[14]: 0 -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -8: t1^t2: 14, 15, 17, -8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -8: except -8: [06:21:43] Done -8: [06:21:43] Test DiscreteValue Vectors 1 ---------------------------- -8: [06:21:43] Expected failure: Value out of range -8: [06:21:43] Expected failure: Value out of range -8: [06:21:43] Expected failure: Value out of range -8: [06:21:43] Expected failure: Value out of range -8: [06:21:43] Expected failure: Value out of range -8: [06:21:43] Test DiscreteValue Vectors 2 ------------------------------ -8: [06:21:43] Test DiscreteValue Vectors 3 --------------------------- -8: [06:21:43] Test DiscreteValue Operations ----------------------------- -8: [06:21:43] Test DiscreteValue Operations 2 -------------------------- -8: [06:21:43] Test SparseIntVect ------------------------------------ -8: [06:21:43] Test SparseIntVect Serialization -------------------------- -8: [06:21:43] Test BitVect Serialization ------------------------------- -8: [06:21:43] Test BitVect to FPS ------------------------------- -8: [06:21:43] Test BitVect to binary string ------------------------------- -8: [06:21:43] Test Similarity Measures BitVect ------------------------------- -8: [06:21:43] Test Similarity Measures SparseBitVect ------------------------------- -8: [06:21:43] Test BitVect with all ones ------------------------------- -8: [06:21:43] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [06:21:43] Test bitmap operations ------------------------------- -8: [06:21:43] Test bitmaps as properties ------------------------------- -8: [06:21:43] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -11: Randomness seeded to: 188728693 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: -16: **************************************** -16: testPointND -16: **************************************** -16: testPointOps3D -16: **************************************** -16: testPointOps2D -16: **************************************** -16: test12D -16: ref1: 0.553665 3.71256 ref2: 2.21211 4.98306 -16: pt1: 1.89146 1.17273 pt2: 3.16911 1.66378 -16: **************************************** -16: test23D -16: **************************************** -16: test3MatMultiply -16: Pt1: 1 0 0 Pt2: 2 0 0 -16: -Pt1: -1 -0 -0 -16: tp1: 0 0 0 tp2: 0 0 0 -16: tp1: 0 0 0 tp2: 0 0 0 -16: tp1: 0 0 3 tp2: 0 0 3 -16: npt1: 0 0 3 npt2: 0 0 4 -16: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 -16: **************************************** -16: testFromQuaternion -16: **************************************** -18: Randomness seeded to: 3731740168 -18: =============================================================================== -18: All tests passed (50 assertions in 5 test cases) -18: -20: [06:21:43] ----------------------------------------- -20: [06:21:43] Testing RDNumerics: vectors and matrices Code -20: [06:21:43] --------------------------------------- -20: [06:21:43] test1Vector -20: [06:21:43] --------------------------------------- -20: [06:21:43] test2Matrix -20: [06:21:43] --------------------------------------- -20: [06:21:43] test3SquareMatrix -20: [06:21:43] --------------------------------------- -20: [06:21:43] test4SymmMatrix - 1/230 Test #4: testRDValue ............................ Passed 0.04 sec - 2/230 Test #6: dictTestsCatch ......................... Passed 0.04 sec - 3/230 Test #7: logTestsCatch .......................... Passed 0.04 sec - 4/230 Test #8: testDataStructs ........................ Passed 0.03 sec - 5/230 Test #9: testFPB ................................ Passed 0.03 sec - 6/230 Test #10: testMultiFPB ........................... Passed 0.03 sec - 7/230 Test #11: catchDataStructs ....................... Passed 0.03 sec - 8/230 Test #16: testTransforms ......................... Passed 0.02 sec - 9/230 Test #18: geometryTestsCatch ..................... Passed 0.02 sec - 10/230 Test #20: testMatrices ........................... Passed 0.01 sec -test 23 - Start 23: pyAlignment - -23: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/testAlignment.py" -23: Working Directory: /build/reproducible-path/rdkit-202409.2/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-202409.2/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer -24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Optimizer -24: Test timeout computed to be: 1500 -test 25 - Start 25: ForceFieldsCatch - -25: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/ForceFieldsCatch -25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField -25: Test timeout computed to be: 1500 -test 26 - Start 26: testUFFForceField - -26: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField -26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/UFF -26: Test timeout computed to be: 1500 -test 27 - Start 27: testMMFFForceField - -27: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/MMFF -27: Test timeout computed to be: 1500 -test 28 - Start 28: pyForceFieldConstraints - -28: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/testConstraints.py" -28: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/Wrap -28: Test timeout computed to be: 1500 -test 29 - Start 29: testDistGeom - -29: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/testDistGeom -29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom -29: Test timeout computed to be: 1500 -test 30 - Start 30: pyDistGeom - -30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/rough_test.py" -30: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/Wrap -30: Test timeout computed to be: 1500 -test 31 - Start 31: graphmolTest1 - -31: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -31: Test timeout computed to be: 1500 -test 32 - Start 32: graphmolcpTest - -32: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest -32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -16791,6 +16696,37 @@ 1: 11 9 1 0 1: M END 1: +16: **************************************** +16: testPointND +16: **************************************** +16: testPointOps3D +16: **************************************** +16: testPointOps2D +16: **************************************** +16: test12D +16: ref1: 0.0407531 3.44936 ref2: 0.469699 1.76095 +16: pt1: 0.67267 1.40945 pt2: 3.59425 4.96011 +16: **************************************** +16: test23D +16: **************************************** +16: test3MatMultiply +16: Pt1: 1 0 0 Pt2: 2 0 0 +16: -Pt1: -1 -0 -0 +16: tp1: 0 0 0 tp2: 0 0 0 +16: tp1: 0 0 0 tp2: 0 0 0 +16: tp1: 0 0 3 tp2: 0 0 3 +16: npt1: 0 0 3 npt2: 0 0 4 +16: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 +16: **************************************** +16: testFromQuaternion +16: **************************************** + 8/230 Test #16: testTransforms ......................... Passed 0.07 sec +test 18 + Start 18: geometryTestsCatch + +18: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch +18: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry +18: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -16935,17 +16871,18 @@ 1: 2 5 1 0 1: M END 1: -22: ----------------------------------------- -22: Testing Alignment Code -22: --------------------------------------- -22: testBasic -22: --------------------------------------- -22: testTriangle -22: --------------------------------------- -22: testFourPts -22: --------------------------------------- -22: testReflection -22: --------------------------------------- +3: static boost any:0.18726 s +18: Randomness seeded to: 3853969523 +18: =============================================================================== +18: All tests passed (50 assertions in 5 test cases) +18: + 9/230 Test #18: geometryTestsCatch ..................... Passed 0.06 sec +test 19 + Start 19: testPyGeometry + +19: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/testGeometry.py" +19: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Geometry/Wrap +19: Test timeout computed to be: 1500 17: *********************************************************** 17: Testing Grid 17: --------------------------------- @@ -16963,44 +16900,100 @@ 17: --------------------------------- 17: testUniformGridIndexing 17: -21: Randomness seeded to: 803419045 + 10/230 Test #17: testGrid ............................... Passed 0.13 sec +test 20 + Start 20: testMatrices + +20: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/testMatrices +20: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 +20: [02:43:32] ----------------------------------------- +20: [02:43:32] Testing RDNumerics: vectors and matrices Code +20: [02:43:32] --------------------------------------- +20: [02:43:32] test1Vector +20: [02:43:32] --------------------------------------- +20: [02:43:32] test2Matrix +20: [02:43:32] --------------------------------------- +20: [02:43:32] test3SquareMatrix +20: [02:43:32] --------------------------------------- +20: [02:43:32] test4SymmMatrix + 11/230 Test #20: testMatrices ........................... Passed 0.03 sec +test 21 + Start 21: testConrec + +21: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/testConrec +21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics +21: Test timeout computed to be: 1500 +21: Randomness seeded to: 598223537 21: =============================================================================== 21: All tests passed (76 assertions in 3 test cases) 21: + 12/230 Test #21: testConrec ............................. Passed 0.11 sec +test 22 + Start 22: testAlignment + +22: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment +22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment +22: Test timeout computed to be: 1500 +22: ----------------------------------------- +22: Testing Alignment Code +22: --------------------------------------- +22: testBasic +22: --------------------------------------- +22: testTriangle +22: --------------------------------------- +22: testFourPts +22: --------------------------------------- +22: testReflection +22: --------------------------------------- + 13/230 Test #22: testAlignment .......................... Passed 0.03 sec +test 23 + Start 23: pyAlignment + +23: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/testAlignment.py" +23: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap +23: Test timeout computed to be: 1500 +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.006s +13: +13: OK + 14/230 Test #13: pyDiscreteValueVect .................... Passed 0.42 sec +test 24 + Start 24: testOptimizer + +24: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer +24: Working Directory: /build/reproducible-path/rdkit-202409.2/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 - 11/230 Test #17: testGrid ............................... Passed 0.05 sec - 12/230 Test #21: testConrec ............................. Passed 0.04 sec - 13/230 Test #22: testAlignment .......................... Passed 0.03 sec - 14/230 Test #24: testOptimizer .......................... Passed 0.03 sec -test 33 - Start 33: graphmolqueryTest - -33: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest -33: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -test 34 - Start 34: graphmolMolOpsTest - -34: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest -34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -test 35 - Start 35: graphmoltestChirality + 15/230 Test #24: testOptimizer .......................... Passed 0.03 sec +test 25 + Start 25: ForceFieldsCatch -35: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality -35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -test 36 - Start 36: graphmoltestPickler +25: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/ForceFieldsCatch +25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField +25: Test timeout computed to be: 1500 +25: Randomness seeded to: 2839551185 +25: =============================================================================== +25: All tests passed (20 assertions in 2 test cases) +25: + 16/230 Test #25: ForceFieldsCatch ....................... Passed 0.14 sec +test 26 + Start 26: testUFFForceField -36: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler -36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 +26: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField +26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/UFF +26: Test timeout computed to be: 1500 +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.019s +14: +14: OK 26: ------------------------------------- 26: Unit tests for force field basics. 26: done @@ -17029,6 +17022,11 @@ 26: done 26: ------------------------------------- 26: Test UFF Parameter objects +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.058s +15: +15: OK 26: ------------------------------------- 26: Test Simple UFF molecule optimization, part 2. 26: done @@ -17047,6 +17045,43 @@ 26: done 26: ------------------------------------- 26: Unit tests for all UFF constraint terms. +19: ........... +19: ---------------------------------------------------------------------- +19: Ran 11 tests in 0.058s +19: +19: OK +19: Testing Geometry wrapper + 17/230 Test #14: pySparseIntVect ........................ Passed 0.70 sec +test 27 + Start 27: testMMFFForceField + +27: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/MMFF +27: Test timeout computed to be: 1500 + 18/230 Test #19: testPyGeometry ......................... Passed 0.58 sec +test 28 + Start 28: pyForceFieldConstraints + +28: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/testConstraints.py" +28: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ForceField/Wrap +28: Test timeout computed to be: 1500 + 19/230 Test #15: pyFPB .................................. Passed 0.75 sec +test 29 + Start 29: testDistGeom + +29: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/testDistGeom +29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom +29: Test timeout computed to be: 1500 + 20/230 Test #2: pyCoordGen .............................***Exception: SegFault 0.89 sec + +test 30 + Start 30: pyDistGeom + +30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/rough_test.py" +30: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DistGeom/Wrap +30: Test timeout computed to be: 1500 +27: ------------------------------------- +27: Official MMFF validation suite. 29: *********************************************************** 29: test1 29: *********************************************************** @@ -17058,68 +17093,386 @@ 29: 1 1 1 0 29: *********************************************************** 29: -32: -32: -32: -32: COPY -27: ------------------------------------- -27: Official MMFF validation suite. -25: Randomness seeded to: 1850659394 -25: =============================================================================== -25: All tests passed (20 assertions in 2 test cases) -25: - 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.04 sec - 16/230 Test #29: testDistGeom ........................... Passed 0.02 sec -test 37 - Start 37: graphmoltestPicklerGlobalSetting - -37: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -test 38 - Start 38: graphmolIterTest + 21/230 Test #29: testDistGeom ........................... Passed 0.05 sec +test 31 + Start 31: graphmolTest1 -38: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest -38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -33: [06:21:43] ---------------------- Test1 - 17/230 Test #32: graphmolcpTest ......................... Passed 0.03 sec -test 39 - Start 39: hanoiTest +31: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +31: Test timeout computed to be: 1500 +1: cyclosporine a +1: RDKit 2D +1: +1: 85 85 0 0 0 0 0 0 0 0999 V2000 +1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4912 -3.8489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.1202 1.6017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.1626 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.6784 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 3 2 1 1 +1: 3 4 1 0 +1: 4 5 2 0 +1: 4 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 8 10 1 0 +1: 10 11 1 0 +1: 11 12 1 0 +1: 12 13 2 0 +1: 12 14 1 0 +1: 14 15 1 0 +1: 15 16 1 0 +1: 16 17 2 0 +1: 16 18 1 0 +1: 18 19 1 0 +1: 19 20 1 0 +1: 20 21 2 0 +1: 20 22 1 0 +1: 22 23 1 0 +1: 23 24 1 0 +1: 24 25 2 0 +1: 24 26 1 0 +1: 26 27 1 0 +1: 27 28 1 0 +1: 28 29 2 0 +1: 28 30 1 0 +1: 30 31 1 0 +1: 31 32 1 0 +1: 32 33 2 0 +1: 32 34 1 0 +1: 34 35 1 0 +1: 35 36 1 0 +1: 36 37 2 0 +1: 36 38 1 0 +1: 38 39 1 0 +1: 39 40 1 0 +1: 40 41 2 0 +1: 40 42 1 0 +1: 43 42 1 6 +1: 43 44 1 0 +1: 44 45 2 0 +1: 44 46 1 0 +1: 43 47 1 0 +1: 47 48 1 0 +1: 48 49 1 6 +1: 48 50 1 0 +1: 50 51 1 0 +1: 51 52 2 0 +1: 52 53 1 0 +1: 47 54 1 1 +1: 42 55 1 0 +1: 39 56 1 6 +1: 56 57 1 0 +1: 56 58 1 0 +1: 38 59 1 0 +1: 35 60 1 6 +1: 60 61 1 0 +1: 61 62 1 0 +1: 61 63 1 0 +1: 34 64 1 0 +1: 31 65 1 6 +1: 65 66 1 0 +1: 66 67 1 0 +1: 66 68 1 0 +1: 30 69 1 0 +1: 27 70 1 6 +1: 23 71 1 6 +1: 19 72 1 6 +1: 72 73 1 0 +1: 73 74 1 0 +1: 73 75 1 0 +1: 18 76 1 0 +1: 15 77 1 6 +1: 77 78 1 0 +1: 77 79 1 0 +1: 11 80 1 6 +1: 80 81 1 0 +1: 81 82 1 0 +1: 81 83 1 0 +1: 10 84 1 0 +1: 6 85 1 0 +1: 46 3 1 0 +1: M END +1: +1: single-double +1: RDKit 2D +1: +1: 17 16 0 0 0 0 0 0 0 0999 V2000 +1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 2 3 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 9 10 1 0 +1: 10 11 2 3 +1: 11 12 1 0 +1: 12 13 2 3 +1: 13 14 1 0 +1: 14 15 2 3 +1: 15 16 1 0 +1: 16 17 1 0 +1: M END +1: +1: cis-trans +1: RDKit 2D +1: +1: 10 9 0 0 0 0 0 0 0 0999 V2000 +1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 2 0 +1: 3 4 1 0 +1: 4 5 2 0 +1: 5 6 1 0 +1: 6 7 2 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 9 10 1 0 +1: M END +1: +1: admntn +1: RDKit 2D +1: +1: 10 12 0 0 0 0 0 0 0 0999 V2000 +1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 6 10 1 0 +1: 8 1 1 0 +1: 9 4 1 0 +1: 10 2 1 0 +1: M END +1: +26: done +26: ------------------------------------- +26: Unit tests for copying UFF ForceFields. +1: github 4845 - nan coordinates but no crash +1: RDKit 2D +1: +1: 42 44 0 0 0 0 0 0 0 0999 V2000 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 2 4 2 0 +1: 4 5 1 0 +1: 5 6 3 0 +1: 6 7 1 0 +1: 7 8 2 0 +1: 8 9 1 0 +1: 9 10 3 0 +1: 10 11 1 0 +1: 11 12 2 0 +1: 12 13 1 0 +1: 13 14 3 0 +1: 14 15 1 0 +1: 15 16 2 0 +1: 16 17 1 0 +1: 16 18 1 0 +1: 12 19 1 0 +1: 19 20 2 0 +1: 20 21 1 0 +1: 20 22 1 0 +1: 19 23 1 0 +1: 23 24 3 0 +1: 24 25 1 0 +1: 25 26 1 0 +1: 26 27 2 0 +1: 27 28 2 0 +1: 26 29 1 0 +1: 29 30 3 0 +1: 8 31 1 0 +1: 31 32 2 0 +1: 32 33 1 0 +1: 32 34 1 0 +1: 31 35 1 0 +1: 35 36 3 0 +1: 36 37 1 0 +1: 37 38 2 0 +1: 37 39 1 0 +1: 39 40 2 0 +1: 40 41 1 0 +1: 40 42 1 0 +1: 39 4 1 0 +1: 15 7 1 0 +1: 30 11 1 0 +1: M END +1: +26: done +26: ------------------------------------- +26: Unit test for UFF butane scan. + 22/230 Test #1: testCoordGen ........................... Passed 1.02 sec +test 32 + Start 32: graphmolcpTest -39: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/hanoiTest -39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test2 -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test3 -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test4 -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test5 -33: [06:21:43] Done! -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test issue 2892580 -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test github issue 53: query molecules not matching [R] -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test queries using qualifiers instead of == -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test extra atom queries -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test extra bond queries -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test num heteroatom neighbor queries -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test atom type queries -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -33: [06:21:43] Done! -33: [06:21:43] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -33: [06:21:43] Done! +32: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest +32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 31: Atoms: 31: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 31: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: @@ -17138,7 +17491,7 @@ 31: 4 5->6 order: 3 31: 5 6->7 order: 1 31: 6 7->8 order: 2 -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17150,15 +17503,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x565F0D4E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565E91A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565DBD4E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D41A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 7# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17170,15 +17523,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x565DE303 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565E91A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565C9303 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D41A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 7# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17190,15 +17543,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x565DE46E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565E91A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565C946E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D41A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 7# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17210,15 +17563,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x565DE4B3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565E91A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565C94B3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D41A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 7# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17230,57 +17583,21 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x565DE5ED in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565E91A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565C95ED in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D41A9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 7# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] Explicit valence for atom # 0 B, 4, is greater than permitted - 18/230 Test #33: graphmolqueryTest ...................... Passed 0.03 sec -test 40 - Start 40: graphmolMemTest1 - -40: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 -40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -31: [06:21:43] Explicit valence for atom # 0 B, 4, is greater than permitted -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing String Pickle Roundtrips. -37: [06:21:43] done -39: [06:21:43] Testing the hanoi sort -39: [06:21:43] populating vectors - 19/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec -test 41 - Start 41: resMolSupplierTest - -41: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest -41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 - 20/230 Test #40: graphmolMemTest1 ....................... Passed 0.02 sec -test 42 - Start 42: molBundleTest - -42: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molBundleTest -42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -35: -------------------------- -35: -------------------------- -35: C/C=C/C(C)Cl -34: 1 1 2 -34: 1 1 1 -34: 2 1 0.75 - 21/230 Test #38: graphmolIterTest ....................... Passed 0.03 sec -test 43 - Start 43: testSGroup - -43: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/testSGroup -43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -34: path: 2 -31: [06:21:43] +31: [02:43:32] Explicit valence for atom # 0 B, 4, is greater than permitted +31: [02:43:32] Explicit valence for atom # 0 B, 4, is greater than permitted +32: +32: +32: +32: COPY +31: [02:43:32] 31: 31: **** 31: Post-condition Violation @@ -17292,21 +17609,34 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x5660F21E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x565EB64B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x565E91B8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 6# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 3# 0x565FA21E in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x565D664B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x565D41B8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 8# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 8# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test github381: thread-safe initialization of the periodic table -31: [06:21:43] done -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [06:21:43] +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test github381: thread-safe initialization of the periodic table + 23/230 Test #32: graphmolcpTest ......................... Passed 0.08 sec +test 33 + Start 33: graphmolqueryTest + +33: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest +33: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +23: ..... +23: ---------------------------------------------------------------------- +23: Ran 5 tests in 0.011s +23: +23: OK +23: Testing Alignment Wrapper code: +31: [02:43:32] done +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17317,15 +17647,15 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x56609901 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x565E91E5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 2# 0x565F4901 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x565D41E5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 6# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17336,18 +17666,18 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x565E88B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x565E91E5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 2# 0x565D38B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x565D41E5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 6# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] done -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [06:21:43] +31: [02:43:32] done +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17358,15 +17688,15 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x56609901 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x565E91EA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 2# 0x565F4901 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x565D41EA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 6# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] +31: [02:43:32] 31: 31: **** 31: Pre-condition Violation @@ -17377,571 +17707,119 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x565E88B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x565E91EA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0xF74D4D43 in /lib/i386-linux-gnu/libc.so.6 +31: 2# 0x565D38B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x565D41EA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0xF748ED43 in /lib/i386-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -31: 6# 0x565E9257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x565D4257 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [06:21:43] done -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test github1453: RWMol.clear() should reset the numBonds count. -31: [06:21:43] done -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test range-based for loops. -31: [06:21:43] done -31: [06:21:43] ------------------------------------- -31: [06:21:43] Test github1642: Atom index type is too low for big molecules. -34: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -34: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -3: static boost any:0.124544 s -34: [06:21:43] Explicit valence for atom # 0 B, 5, is greater than permitted -34: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [06:21:43] Explicit valence for atom # 1 Si, 7, is greater than permitted -26: done -26: ------------------------------------- -26: Unit tests for copying UFF ForceFields. - 22/230 Test #42: molBundleTest .......................... Passed 0.03 sec -test 44 - Start 44: test-valgrind - -44: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/test-valgrind -44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -35: [06:21:43] Conflicting single bond directions around double bond at index 2. -35: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [06:21:43] Conflicting single bond directions around double bond at index 4. -35: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [06:21:43] Conflicting single bond directions around double bond at index 15. -35: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [06:21:43] Conflicting single bond directions around double bond at index 2. -35: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [06:21:43] Conflicting single bond directions around double bond at index 1. -35: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -26: done -26: ------------------------------------- -26: Unit test for UFF butane scan. - 23/230 Test #43: testSGroup ............................. Passed 0.05 sec -test 45 - Start 45: graphmolTestsCatch - -45: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 - 24/230 Test #44: test-valgrind .......................... Passed 0.03 sec -test 46 - Start 46: graphmolOrganometallicsCatch - -46: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -35: -------------------------------------------------- - 25/230 Test #35: graphmoltestChirality .................. Passed 0.10 sec -test 47 - Start 47: graphmolSGroupCatch +31: [02:43:32] done +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test github1453: RWMol.clear() should reset the numBonds count. +31: [02:43:32] done +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test range-based for loops. +31: [02:43:32] done +31: [02:43:32] ------------------------------------- +31: [02:43:32] Test github1642: Atom index type is too low for big molecules. +33: [02:43:32] ---------------------- Test1 +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test2 +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test3 +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test4 +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test5 +33: [02:43:33] Done! +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test issue 2892580 +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test github issue 53: query molecules not matching [R] +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test queries using qualifiers instead of == +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test extra atom queries +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test extra bond queries +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test num heteroatom neighbor queries +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test atom type queries +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +33: [02:43:33] Done! +33: [02:43:33] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +33: [02:43:33] Done! + 24/230 Test #33: graphmolqueryTest ...................... Passed 0.13 sec +test 34 + Start 34: graphmolMolOpsTest -47: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch -47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing reading existing pickle file (v2). -45: Randomness seeded to: 1271012978 -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 N, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [06:21:43] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [06:21:43] non-ring atom 2 marked aromatic -45: [06:21:43] non-ring atom 2 marked aromatic -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [06:21:43] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [06:21:43] Explicit valence for atom # 4 F, 2, is greater than permitted -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 6 7 8 -47: Randomness seeded to: 925100057 -47: =============================================================================== -47: All tests passed (136 assertions in 8 test cases) -47: -45: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -45: [06:21:43] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [06:21:43] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [06:21:43] WARNING: not removing hydrogen atom with wedged bond -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors - 26/230 Test #47: graphmolSGroupCatch .................... Passed 0.04 sec -test 48 - Start 48: graphmolAdjustQueryCatch +34: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest +34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 + 25/230 Test #23: pyAlignment ............................ Passed 0.80 sec +test 35 + Start 35: graphmoltestChirality -48: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.006s -13: -13: OK -34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors -45: [06:21:43] Unreasonable formal charge on atom # 0. -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.007s -14: -14: OK -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no atom -45: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: at -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x566513D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no owner -45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -45: Failed Expression: dp_mol -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x5665146F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: atom not associated with this molecule -45: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: &at->getOwningMol() == this -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x56651518 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no atom -45: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: at -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x56651640 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no owner -45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -45: Failed Expression: dp_mol -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x566516E4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: atom not associated with this molecule -45: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: &at->getOwningMol() == this -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x56651795 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no atom -45: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: at -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x56652207 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: no owner -45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -45: Failed Expression: dp_mol -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x5665194B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: atom not associated with this molecule -45: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: &at->getOwningMol() == this -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x566519FC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: null atom passed in -45: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: atom_pin -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x566521DC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: cannot take ownership of an atom which already has an owner -45: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x56651D62 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: cannot take ownership of an bond which already has an owner -45: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp -45: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x566521BD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -46: Randomness seeded to: 2208603277 -46: =============================================================================== -46: All tests passed (62 assertions in 6 test cases) -46: -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [06:21:43] WARNING: not removing hydrogen atom without neighbors -45: [06:21:43] Explicit valence for atom # 1 F greater than permitted -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: plain atoms have no Query -45: Violation occurred on line 691 in file ./Code/GraphMol/Atom.cpp -45: Failed Expression: 0 -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x565F7044 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** - 27/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.06 sec -test 49 - Start 49: chiralityTestsCatch +35: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality +35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 + 26/230 Test #28: pyForceFieldConstraints ................***Exception: SegFault 0.49 sec -49: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch -49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -45: Pre-condition Violation -45: plain atoms have no Query -45: Violation occurred on line 696 in file ./Code/GraphMol/Atom.cpp -45: Failed Expression: 0 -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x565F70D4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: plain bonds have no Query -45: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp -45: Failed Expression: 0 -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x565F6DA9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] -45: -45: **** -45: Pre-condition Violation -45: plain bonds have no query -45: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp -45: Failed Expression: 0 -45: ---------- -45: Stacktrace: -45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x565F6E39 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x566A343B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x566A411F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x566A4784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x56673704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x56673A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x565E8546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0xF73DCD43 in /lib/i386-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -45: 12# 0x565E8587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 - 28/230 Test #2: pyCoordGen .............................***Exception: SegFault 0.25 sec +test 36 + Start 36: graphmoltestPickler -test 50 - Start 50: canonTestsCatch +36: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler +36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +34: 1 1 2 +34: 1 1 1 +34: 2 1 0.75 +34: path: 2 +35: -------------------------- +35: -------------------------- +35: C/C=C/C(C)Cl +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing String Pickle Roundtrips. +34: [02:43:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +34: [02:43:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +34: [02:43:33] Explicit valence for atom # 0 B, 5, is greater than permitted +34: [02:43:33] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [02:43:33] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [02:43:33] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [02:43:33] Explicit valence for atom # 1 Si, 7, is greater than permitted +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing reading existing pickle file (v2). +35: [02:43:33] Conflicting single bond directions around double bond at index 2. +35: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [02:43:33] Conflicting single bond directions around double bond at index 4. +35: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [02:43:33] Conflicting single bond directions around double bond at index 15. +35: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [02:43:33] Conflicting single bond directions around double bond at index 2. +35: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [02:43:33] Conflicting single bond directions around double bond at index 1. +35: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. +3: dynamic boost any:0.739413 s +35: -------------------------------------------------- + 27/230 Test #35: graphmoltestChirality .................. Passed 0.33 sec +test 37 + Start 37: graphmoltestPicklerGlobalSetting -50: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Unusual charge on atom 0 number of radical electrons set to zero -45: [06:21:43] Unusual charge on atom 0 number of radical electrons set to zero -45: [06:21:43] Unusual charge on atom 0 number of radical electrons set to zero -45: [06:21:43] non-ring atom 0 marked aromatic -45: [06:21:43] non-ring atom 0 marked aromatic -45: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing combining molecules using pickles. +37: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing combining molecules using pickles. 36: Atoms: 36: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -17958,79 +17836,43 @@ 36: 4 4->5 order: 1 36: 5 5->6 order: 1 36: 6 6->3 order: 1 -45: [06:21:43] Explicit valence for atom # 9 C, 5, is greater than permitted -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Issue164: Roundtrip Pickle Failure. -45: [06:21:43] Explicit valence for atom # 3 N, 4, is greater than permitted -45: [06:21:43] Explicit valence for atom # 15 C, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 11 C, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [06:21:43] Explicit valence for atom # 9 C, 6, is greater than permitted -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 7 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 3 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 3 7 -45: [06:21:43] Can't kekulize mol. Unkekulized atoms: 3 7 -34: [06:21:43] non-ring atom 0 marked aromatic -34: [06:21:43] non-ring atom 0 marked aromatic - 29/230 Test #13: pyDiscreteValueVect .................... Passed 0.24 sec -test 51 - Start 51: moliteratorTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.007s -15: -15: OK -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Issue219: Pickle Failure with Conformations. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Issue220: Pickle problems with bond stereochemistry. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing query serialization. -36: [06:21:43] C=[$(C=O)] -36: [06:21:43] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing radical handling in pickles. -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 2788233. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 3202580. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Issue164: Roundtrip Pickle Failure. +30: ...... +30: ---------------------------------------------------------------------- +30: Ran 6 tests in 0.010s +30: +30: OK +34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Issue219: Pickle Failure with Conformations. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Issue220: Pickle problems with bond stereochemistry. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing query serialization. +36: [02:43:33] C=[$(C=O)] +36: [02:43:33] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing radical handling in pickles. +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 2788233. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 3202580. 36: mass! 13.0034 -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 3316407. -23: ..... -23: ---------------------------------------------------------------------- -23: Ran 5 tests in 0.002s -23: -23: OK -23: Testing Alignment Wrapper code: -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... - 30/230 Test #14: pySparseIntVect ........................ Passed 0.24 sec -test 52 - Start 52: queryTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/queryTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 3496759. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 3316407. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 3496759. 36: smi match: *C *C 36: smi match: **=* **=* 36: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -18039,8 +17881,16 @@ 36: smi match: O=COC=O O=COC=O 36: smi match: OO OO 36: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +37: [02:43:33] done 36: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 36: smi match: nnnOC=O nnnOC=O + 28/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec +test 38 + Start 38: graphmolIterTest + +38: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest +38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 36: smi match: *=C=N *=C=N 36: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 36: smi match: SP(S)=S SP(S)=S @@ -18053,24 +17903,16 @@ 36: smi match: CC(=N)Cl CC(=N)Cl 36: smi match: N=O N=O 36: smi match: ** ** -45: [06:21:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -34: [06:21:43] Conflicting single bond directions around double bond at index 17. -34: [06:21:43] BondStereo set to STEREONONE and single bond directions set to NONE. -34: starting ring finding 36: smi match: N=C=N N=C=N 36: smi match: [C-]#[NH+] [C-]#[NH+] -34: done 36: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 36: smi match: N#CC[OH] N#CC[OH] -34: starting ring finding 36: smi match: N#CC=O N#CC=O 36: smi match: N#CS(=O)=O N#CS(=O)=O 36: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 36: smi match: N#CN=N N#CN=N 36: smi match: N=NCC=O N=NCC=O 36: smi match: CCCCCCC CCCCCCC -34: done -34: starting ring finding 36: smi match: OCCOCCO OCCOCCO 36: smi match: SS SS 36: smi match: [SH] [SH] @@ -18082,27 +17924,13 @@ 36: smi match: cC[N+] cC[N+] 36: smi match: C*C=S C*C=S 36: smi match: N[CH2]C#N N[CH2]C#N -34: done 36: smi match: O=C1CCO1 O=C1CCO1 36: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] -34: 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 -34: starting sanitization 36: smi match: O=C1CCN1 O=C1CCN1 36: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 36: smi match: C=CC=CC=CC=C C=CC=CC=CC=C -48: Randomness seeded to: 1574178781 -48: =============================================================================== -48: All tests passed (281 assertions in 10 test cases) -48: 36: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 36: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 - 31/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.06 sec -test 53 - Start 53: molbundleTestsCatch - -53: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molbundleTestsCatch -53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -53: Test timeout computed to be: 1500 36: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 36: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 36: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 @@ -18111,20 +17939,9 @@ 36: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 36: smi match: N~NC=O N~NC=O 36: smi match: *=N~C *=N~C -51: Randomness seeded to: 503313805 -51: =============================================================================== -51: All tests passed (14 assertions in 4 test cases) -51: 36: smi match: CO*(=O)=O CO*(=O)=O 36: smi match: * * 36: smi match: * * - 32/230 Test #51: moliteratorTestsCatch .................. Passed 0.03 sec -test 54 - Start 54: pickleTestsCatch - -54: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/pickleTestsCatch -54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -54: Test timeout computed to be: 1500 36: smi match: *C=C *C=C 36: smi match: N#CS N#CS 36: smi match: *C=S *C=S @@ -18138,20 +17955,6 @@ 36: smi match: C=C(C=O)C=O C=C(C=O)C=O 36: smi match: N=CC=O N=CC=O 36: smi match: *C(C=O)C=O *C(C=O)C=O - 33/230 Test #15: pyFPB .................................. Passed 0.27 sec - 34/230 Test #23: pyAlignment ............................ Passed 0.25 sec -test 55 - Start 55: tableTestsCatch - -55: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/tableTestsCatch -55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -55: Test timeout computed to be: 1500 -test 56 - Start 56: molopsTestsCatch - -56: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molopsTestsCatch -56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol -56: Test timeout computed to be: 1500 36: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 36: smi match: O=CC=CC=O O=CC=CC=O 36: smi match: O=CN(O)C=O O=CN(O)C=O @@ -18186,6 +17989,8 @@ 36: smi match: C=CS C=CS 36: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 36: smi match: C=NCO C=NCO +34: [02:43:33] non-ring atom 0 marked aromatic +34: [02:43:33] non-ring atom 0 marked aromatic 36: smi match: C=NC=O C=NC=O 36: smi match: C=NN C=NN 36: smi match: C=NN=C C=NN=C @@ -18200,21 +18005,6 @@ 36: smi match: N=C(N)S N=C(N)S 36: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 36: smi match: NC=S NC=S -52: Randomness seeded to: 578273301 -52: =============================================================================== -52: All tests passed (10 assertions in 1 test case) -52: -34: done -34: starting sanitization -49: Randomness seeded to: 3339288660 -49: [06:21:43] unable to set wavy bonds for double bonds: 3 - 35/230 Test #52: queryTestsCatch ........................ Passed 0.04 sec -test 57 - Start 57: smiTest1 - -57: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -57: Test timeout computed to be: 1500 36: smi match: NC(N)=S NC(N)=S 36: smi match: C=CN C=CN 36: smi match: NOC=O NOC=O @@ -18232,17 +18022,6 @@ 36: smi match: NOC(=O)O NOC(=O)O 36: smi match: *C(O)=S *C(O)=S 36: smi match: C=CO C=CO -34: done -34: starting ring finding -34: done -34: starting ring finding -34: done -34: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -30: ...... -30: ---------------------------------------------------------------------- -30: Ran 6 tests in 0.001s -30: -30: OK 36: smi match: ON=CC=NO ON=CC=NO 36: smi match: *C[SH](=O)=O *C[SH](=O)=O 36: smi match: OS(=O)=O OS(=O)=O @@ -18262,25 +18041,21 @@ 36: smi match: cS(=O)(=O)O cS(=O)(=O)O 36: smi match: *c1ccccn1=O *c1ccccn1=O 36: smi match: *c1ccccn1 *c1ccccn1 -53: Randomness seeded to: 689265527 -53: =============================================================================== -53: All tests passed (6 assertions in 1 test case) -53: 36: smi match: *c1nccccn1 *c1nccccn1 36: smi match: C1COCOC1 C1COCOC1 36: smi match: C=S C=S - 36/230 Test #53: molbundleTestsCatch .................... Passed 0.03 sec -test 58 - Start 58: smiTest2 - -58: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -58: Test timeout computed to be: 1500 36: smi match: c=S c=S 36: smi match: S=CS S=CS 36: smi match: C=CN(=O)=O C=CN(=O)=O 36: smi match: C=CN(=O)O C=CN(=O)O 36: smi match: N=CC=O N=CC=O + 29/230 Test #30: pyDistGeom ............................. Passed 0.84 sec +test 39 + Start 39: hanoiTest + +39: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/hanoiTest +39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 36: smi match: C=CS C=CS 36: smi match: SC(S)(S)S SC(S)(S)S 36: smi match: OS(O)(O)O OS(O)(O)O @@ -18293,29 +18068,12 @@ 36: smi match: N=C(S)S N=C(S)S 36: smi match: N=C(=N)S N=C(=N)S 36: smi match: O=N=O O=N=O -19: ........... -19: ---------------------------------------------------------------------- -19: Ran 11 tests in 0.037s -19: -19: OK -19: Testing Geometry wrapper 36: smi match: O=NO O=NO 36: smi match: ONO ONO -55: Randomness seeded to: 1402918724 -55: =============================================================================== -55: All tests passed (7 assertions in 2 test cases) -55: 36: smi match: C1SCS1 C1SCS1 36: smi match: N=C=S N=C=S 36: smi match: N=C=N N=C=N 36: smi match: C1N=N1 C1N=N1 - 37/230 Test #55: tableTestsCatch ........................ Passed 0.03 sec -test 59 - Start 59: cxsmilesTest - -59: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -59: Test timeout computed to be: 1500 36: smi match: *CS *CS 36: smi match: SC(S)=C(S)S SC(S)=C(S)S 36: smi match: N=CC=NO N=CC=NO @@ -18328,235 +18086,28 @@ 36: smi match: N#CS N#CS 36: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 36: smi match: c=N c=N -45: [06:21:43] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [06:21:43] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [06:21:43] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 36: smi match: C1COCO1 C1COCO1 -49: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 36: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O -49: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 36: smi match: O=CC=O O=CC=O 36: smi match: O=CNOC=O O=CNOC=O 36: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 36: smi match: ONO ONO 36: smi match: ON(~O)~O ON(~O)~O 36: smi match: OC1COC(O)C1 OC1COC(O)C1 -54: Randomness seeded to: 2729619097 -54: =============================================================================== -54: All tests passed (45 assertions in 4 test cases) -54: 36: smi match: OC1CCOC1O OC1CCOC1O 36: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 36: smi match: N=[N+]=N N=[N+]=N 36: smi match: N#CN N#CN -1: cyclosporine a -1: RDKit 2D -1: -1: 85 85 0 0 0 0 0 0 0 0999 V2000 -1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4912 -3.8489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.1202 1.6017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.1626 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.6784 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 3 2 1 1 -1: 3 4 1 0 -1: 4 5 2 0 -1: 4 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 8 10 1 0 -1: 10 11 1 0 -1: 11 12 1 0 -1: 12 13 2 0 -1: 12 14 1 0 -1: 14 15 1 0 -1: 15 16 1 0 -1: 16 17 2 0 -1: 16 18 1 0 -1: 18 19 1 0 -1: 19 20 1 0 -1: 20 21 2 0 -1: 20 22 1 0 -1: 22 23 1 0 -1: 23 24 1 0 -1: 24 25 2 0 -1: 24 26 1 0 -1: 26 27 1 0 -1: 27 28 1 0 -1: 28 29 2 0 -1: 28 30 1 0 -1: 30 31 1 0 -1: 31 32 1 0 -1: 32 33 2 0 -1: 32 34 1 0 -1: 34 35 1 0 -1: 35 36 1 0 -1: 36 37 2 0 -1: 36 38 1 0 -1: 38 39 1 0 -1: 39 40 1 0 -1: 40 41 2 0 -1: 40 42 1 0 -1: 43 42 1 6 -1: 43 44 1 0 -1: 44 45 2 0 -1: 44 46 1 0 -1: 43 47 1 0 -1: 47 48 1 0 -1: 48 49 1 6 -1: 48 50 1 0 -1: 50 51 1 0 -1: 51 52 2 0 -1: 52 53 1 0 -1: 47 54 1 1 -1: 42 55 1 0 -1: 39 56 1 6 -1: 56 57 1 0 -1: 56 58 1 0 -1: 38 59 1 0 -1: 35 60 1 6 -1: 60 61 1 0 -1: 61 62 1 0 -1: 61 63 1 0 -1: 34 64 1 0 -1: 31 65 1 6 -1: 65 66 1 0 -1: 66 67 1 0 -1: 66 68 1 0 -1: 30 69 1 0 -1: 27 70 1 6 -1: 23 71 1 6 -1: 19 72 1 6 -1: 72 73 1 0 -1: 73 74 1 0 -1: 73 75 1 0 -1: 18 76 1 0 -1: 15 77 1 6 -1: 77 78 1 0 -1: 77 79 1 0 -1: 11 80 1 6 -1: 80 81 1 0 -1: 81 82 1 0 -1: 81 83 1 0 -1: 10 84 1 0 -1: 6 85 1 0 -1: 46 3 1 0 -1: M END -1: -45: [06:21:43] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -45: [06:21:43] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -45: [06:21:43] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom 36: smi match: C=NN=C C=NN=C 36: smi match: *CCN(C)C *CCN(C)C -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [06:21:43] SMILES Parse Error: syntax error while parsing: - -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [06:21:43] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' - 38/230 Test #54: pickleTestsCatch ....................... Passed 0.04 sec -test 60 - Start 60: smaTest1 - -60: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -60: Test timeout computed to be: 1500 -45: [06:21:43] non-ring atom 0 marked aromatic 36: smi match: CNN CNN 36: smi match: *CC *CC 36: smi match: OCS OCS 36: smi match: C1NO1 C1NO1 36: smi match: COS(C)(=O)=O COS(C)(=O)=O +3: static RDAny:0.097796 s +34: [02:43:33] Conflicting single bond directions around double bond at index 17. +34: [02:43:33] BondStereo set to STEREONONE and single bond directions set to NONE. 36: smi match: C1CO1 C1CO1 36: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 36: smi match: *C(*)=C *C(*)=C @@ -18568,96 +18119,16 @@ 36: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 36: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 36: smi match: *N *N -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -58: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' -56: Randomness seeded to: 2196661678 -56: =============================================================================== -56: All tests passed (72 assertions in 4 test cases) -56: -1: single-double -1: RDKit 2D -1: -1: 17 16 0 0 0 0 0 0 0 0999 V2000 -1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 2 3 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 9 10 1 0 -1: 10 11 2 3 -1: 11 12 1 0 -1: 12 13 2 3 -1: 13 14 1 0 -1: 14 15 2 3 -1: 15 16 1 0 -1: 16 17 1 0 -1: M END -1: -1: cis-trans -1: RDKit 2D -1: -1: 10 9 0 0 0 0 0 0 0 0999 V2000 -1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 2 0 -1: 3 4 1 0 -1: 4 5 2 0 -1: 5 6 1 0 -1: 6 7 2 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 9 10 1 0 -1: M END -1: - 39/230 Test #56: molopsTestsCatch ....................... Passed 0.03 sec - 40/230 Test #58: smiTest2 ............................... Passed 0.02 sec -test 61 - Start 61: smiTestCatch - -61: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -61: Test timeout computed to be: 1500 -test 62 - Start 62: nontetrahedralCatch - -62: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -62: Test timeout computed to be: 1500 -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 36: smi match: *P *P 36: smi match: *S *S 36: smi match: *C(*)(*)C=C *C(*)(*)C=C + 30/230 Test #38: graphmolIterTest ....................... Passed 0.09 sec +test 40 + Start 40: graphmolMemTest1 + +40: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 +40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 36: smi match: *C(*)(*)C=C *C(*)(*)C=C 36: smi match: *C(*)C=C *C(*)C=C 36: smi match: *CC=C *CC=C @@ -18684,44 +18155,6 @@ 36: smi match: *C(*)(*)O *C(*)(*)O 36: smi match: COS(O)(=O)=O COS(O)(=O)=O 36: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] -1: admntn -1: RDKit 2D -1: -1: 10 12 0 0 0 0 0 0 0 0999 V2000 -1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 6 10 1 0 -1: 8 1 1 0 -1: 9 4 1 0 -1: 10 2 1 0 -1: M END -1: -34: [06:21:43] WARNING: not removing hydrogen atom with dummy atom neighbors -34: ------------------------------- -34: [06:21:43] Explicit valence for atom # 0 N, 4, is greater than permitted - 41/230 Test #30: pyDistGeom ............................. Passed 0.27 sec -test 63 - Start 63: v2smiTestCatch - -63: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 36: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: *C(*)(*)C=O *C(*)(*)C=O @@ -18730,40 +18163,36 @@ 36: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 36: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 36: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O - 42/230 Test #28: pyForceFieldConstraints ................***Exception: SegFault 0.28 sec - -test 64 - Start 64: testDepictor - -64: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor -64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor -64: Test timeout computed to be: 1500 36: smi match: *C[SH](=O)=O *C[SH](=O)=O +34: starting ring finding +34: done +34: starting ring finding +34: done +34: starting ring finding +34: done +34: 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 +34: starting sanitization +39: [02:43:33] Testing the hanoi sort +39: [02:43:33] populating vectors 36: smi match: * * 36: smi match: *1CC1 *1CC1 36: smi match: O=COC=O O=COC=O 36: smi match: N=C=O N=C=O 36: smi match: N=C=S N=C=S 36: smi match: O~O O~O -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors + 31/230 Test #40: graphmolMemTest1 ....................... Passed 0.04 sec +test 41 + Start 41: resMolSupplierTest + +41: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest +41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 36: smi match: N~[SiH4] N~[SiH4] 36: smi match: *P *P 36: smi match: C=N=N C=N=N 36: smi match: *N#[NH+] *N#[NH+] 36: smi match: *S* *S* 36: smi match: ** ** - 43/230 Test #19: testPyGeometry ......................... Passed 0.31 sec -test 65 - Start 65: depictorCatch - -65: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch -65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -34: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [06:21:43] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -34: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [06:21:43] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: smi match: *CC* *CC* 36: smi match: *O[SiH3] *O[SiH3] 36: smi match: *OS(*)~O *OS(*)~O @@ -18774,51 +18203,36 @@ 36: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 36: smi match: *OCC#N *OCC#N 36: smi match: **C=C **C=C -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 36: smi match: C=C[O-] C=C[O-] 36: smi match: C=CO C=CO -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors 36: smi match: * * 36: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 36: smi match: O=COn1ccnc1 O=COn1ccnc1 36: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 36: smi match: CC(C)(C)S CC(C)(C)S -49: [06:21:43] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 36: 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 -49: [06:21:43] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. 36: smi match: [CH]=O [CH]=O +34: done 36: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 36: smi match: SS SS 36: smi match: [SH] [SH] 36: smi match: *C* *C* +34: starting sanitization 36: smi match: * * 36: smi match: C[nH3+] C[nH3+] 36: smi match: cC(=N)[NH2] cC(=N)[NH2] 36: smi match: O=CN[OH] O=CN[OH] -57: [06:21:43] WARNING: not removing hydrogen atom without neighbors 36: smi match: NN NN -57: [06:21:43] Invalid chiral specification on atom 0 -57: [06:21:43] Invalid chiral specification on atom 0 -57: [06:21:43] Invalid chiral specification on atom 0 -57: [06:21:43] Invalid chiral specification on atom 0 -57: [06:21:43] Invalid chiral specification on atom 0 36: smi match: * * 36: smi match: *OP(=O)O* *OP(=O)O* 36: smi match: * * -49: [06:21:43] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 36: smi match: * * 36: smi match: * * 36: smi match: *N=C(*)* *N=C(*)* 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: CSC=O CSC=O 36: smi match: * * +34: done 36: smi match: O=CCl O=CCl 36: smi match: *** *** 36: smi match: *C=O *C=O @@ -18828,13 +18242,912 @@ 36: smi match: C[OH] C[OH] 36: smi match: C[CH]=O C[CH]=O 36: smi match: *=* *=* +26: done 36: smi match: *C *C -34: [06:21:43] WARNING: not removing hydrogen atom with dummy atom neighbors 36: smi match: C#C C#C -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 36: smi match: *[CH]C=C *[CH]C=C 36: smi match: cCC(=O)[OH] cCC(=O)[OH] -59: Randomness seeded to: 3468599647 +36: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] +36: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +36: smi match: C=CC(=O)[OH] C=CC(=O)[OH] +36: smi match: N#CC(=O)[OH] N#CC(=O)[OH] +36: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +34: starting ring finding +34: done +34: starting ring finding +34: done +34: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 + 32/230 Test #26: testUFFForceField ...................... Passed 1.18 sec +test 42 + Start 42: molBundleTest + +42: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molBundleTest +42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +36: smi match: *N(*)C*=O *N(*)C*=O +36: smi match: O=*C[OH] O=*C[OH] +36: smi match: *=C*=O *=C*=O +36: smi match: *=CC#N *=CC#N +36: smi match: *C[OH] *C[OH] +36: smi match: ** ** +36: smi match: *C[OH] *C[OH] +36: smi match: *C(*)=O *C(*)=O +36: smi match: * * +36: smi match: *CC(=O)[OH] *CC(=O)[OH] +36: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +36: smi match: *c *c +36: smi match: CN(C)c CN(C)c +36: smi match: c c +36: smi match: *c *c +36: smi match: *c *c +36: smi match: **:*cF **:*cF +36: smi match: cB([OH])[OH] cB([OH])[OH] +36: smi match: N~N~N N~N~N +36: smi match: *N=N* *N=N* +36: smi match: *CC[OH] *CC[OH] +36: smi match: *CC[OH] *CC[OH] +36: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +36: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +36: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +36: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +36: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +36: smi match: *OC(*)=O *OC(*)=O +36: smi match: *C(=O)[OH] *C(=O)[OH] +36: smi match: O=C[OH] O=C[OH] +36: smi match: *OC(=O)O* *OC(=O)O* +36: smi match: * * +36: smi match: *OC(=O)Cl *OC(=O)Cl +36: smi match: *C#N *C#N +36: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +36: smi match: SS SS +36: smi match: * * +36: smi match: *=* *=* +34: [02:43:33] WARNING: not removing hydrogen atom with dummy atom neighbors +34: ------------------------------- +36: smi match: *=* *=* +36: smi match: *=* *=* +36: smi match: *=* *=* +36: smi match: C1CO1 C1CO1 +34: [02:43:33] Explicit valence for atom # 0 N, 4, is greater than permitted +36: smi match: *OC(*)=O *OC(*)=O +36: smi match: * * +36: smi match: *O*[OH] *O*[OH] +36: smi match: COC(C)(C)O COC(C)(C)O +36: smi match: *[OH] *[OH] +36: smi match: ** ** +36: smi match: C=N[NH2] C=N[NH2] +36: smi match: C=NC=O C=NC=O +36: smi match: * * +36: smi match: C#NC C#NC +36: smi match: CN=C=O CN=C=O +36: smi match: CN=C=S CN=C=S +36: smi match: *OC(*)(*)O* *OC(*)(*)O* +36: smi match: *C(*)=O *C(*)=O +36: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +36: smi match: *~*=O *~*=O +36: smi match: *~*=O *~*=O +36: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] + 33/230 Test #42: molBundleTest .......................... Passed 0.09 sec +test 43 + Start 43: testSGroup + +43: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/testSGroup +43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +36: smi match: * * +36: smi match: *C#N *C#N +36: smi match: *N(=O)~O *N(=O)~O +36: smi match: N N +36: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +36: smi match: C=NO C=NO +36: smi match: O~O O~O +36: smi match: c[OH] c[OH] +36: smi match: O=P(~[OH])~O O=P(~[OH])~O +36: smi match: CO~P(=O)~O CO~P(=O)~O +36: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +36: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +36: smi match: O=P(~O)~O O=P(~O)~O +36: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +36: smi match: C[NH2] C[NH2] +36: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +36: smi match: * * +36: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +36: smi match: CS(C)~O CS(C)~O +36: smi match: CS(C)(~O)~O CS(C)(~O)~O +36: smi match: CS(N)(~O)~O CS(N)(~O)~O +36: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +36: smi match: COS(C)(~O)~O COS(C)(~O)~O +36: smi match: *S(C)(~O)~O *S(C)(~O)~O +36: smi match: CN(C)C CN(C)C +36: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +36: smi match: *C(*)=S *C(*)=S +34: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [02:43:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +34: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [02:43:33] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: smi match: *OC(*)=S *OC(*)=S +36: smi match: * * +36: smi match: C[SH] C[SH] +36: smi match: c[SH] c[SH] +36: smi match: NC(N)=S NC(N)=S +36: smi match: * * +36: smi match: ***** ***** +36: smi match: NC(N)=O NC(N)=O +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 280. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing sf.net issue 285. +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Github2441: Add RDProps interface to Conformers. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Issue2510: Pickle Confs as double. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing loading pickled mols with conformers +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing conformer reading/writing options +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing property reading options +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing property reading options +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing boost::serialization integration +36: [02:43:33] done +36: [02:43:33] ------------------------------------- +36: [02:43:33] Testing github issue 6036 + 34/230 Test #36: graphmoltestPickler .................... Passed 0.67 sec +test 44 + Start 44: test-valgrind + +44: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/test-valgrind +44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +34: [02:43:33] WARNING: not removing hydrogen atom with dummy atom neighbors + 35/230 Test #44: test-valgrind .......................... Passed 0.07 sec +test 45 + Start 45: graphmolTestsCatch + +45: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +45: Randomness seeded to: 3048213071 +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] Explicit valence for atom # 1 N, 5, is greater than permitted + 36/230 Test #43: testSGroup ............................. Passed 0.18 sec +test 46 + Start 46: graphmolOrganometallicsCatch + +46: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +45: [02:43:33] Explicit valence for atom # 1 N, 6, is greater than permitted +45: [02:43:33] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [02:43:33] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [02:43:33] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [02:43:33] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [02:43:33] non-ring atom 2 marked aromatic +45: [02:43:33] non-ring atom 2 marked aromatic +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [02:43:33] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [02:43:33] Explicit valence for atom # 4 F, 2, is greater than permitted +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 +45: [02:43:33] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [02:43:33] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [02:43:33] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [02:43:33] WARNING: not removing hydrogen atom with wedged bond +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] Unreasonable formal charge on atom # 0. +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no atom +45: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: at +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B03D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no owner +45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +45: Failed Expression: dp_mol +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B046F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: atom not associated with this molecule +45: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: &at->getOwningMol() == this +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B0518 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no atom +45: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: at +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B0640 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no owner +45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +45: Failed Expression: dp_mol +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B06E4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: atom not associated with this molecule +45: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: &at->getOwningMol() == this +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B0795 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no atom +45: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: at +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B1207 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: no owner +45: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +45: Failed Expression: dp_mol +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B094B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: atom not associated with this molecule +45: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: &at->getOwningMol() == this +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B09FC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: null atom passed in +45: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: atom_pin +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B11DC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: cannot take ownership of an atom which already has an owner +45: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B0D62 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: cannot take ownership of an bond which already has an owner +45: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp +45: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566B11BD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:33] WARNING: not removing hydrogen atom without neighbors +45: [02:43:33] Explicit valence for atom # 1 F greater than permitted +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: plain atoms have no Query +45: Violation occurred on line 691 in file ./Code/GraphMol/Atom.cpp +45: Failed Expression: 0 +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x56656044 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: plain atoms have no Query +45: Violation occurred on line 696 in file ./Code/GraphMol/Atom.cpp +45: Failed Expression: 0 +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x566560D4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: plain bonds have no Query +45: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp +45: Failed Expression: 0 +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x56655DA9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] +45: +45: **** +45: Pre-condition Violation +45: plain bonds have no query +45: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp +45: Failed Expression: 0 +45: ---------- +45: Stacktrace: +45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x56655E39 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x5670243B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x5670311F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x56703784 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x566D2704 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x566D2A92 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x56647546 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0xF738ED43 in /lib/i386-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +45: 12# 0x56647587 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [02:43:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:34] Unusual charge on atom 0 number of radical electrons set to zero +45: [02:43:34] Unusual charge on atom 0 number of radical electrons set to zero +45: [02:43:34] Unusual charge on atom 0 number of radical electrons set to zero +45: [02:43:34] non-ring atom 0 marked aromatic +45: [02:43:34] non-ring atom 0 marked aromatic +45: [02:43:34] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 3 N, 4, is greater than permitted +45: [02:43:34] Explicit valence for atom # 15 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 11 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [02:43:34] Explicit valence for atom # 9 C, 6, is greater than permitted +45: [02:43:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [02:43:34] Can't kekulize mol. Unkekulized atoms: 7 +45: [02:43:34] Can't kekulize mol. Unkekulized atoms: 3 +45: [02:43:34] Can't kekulize mol. Unkekulized atoms: 3 7 +45: [02:43:34] Can't kekulize mol. Unkekulized atoms: 3 7 +45: [02:43:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [02:43:34] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [02:43:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [02:43:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +39: [02:43:34] sorting (hanoi sort) vectors +46: Randomness seeded to: 2677325308 +46: =============================================================================== +46: All tests passed (62 assertions in 6 test cases) +46: +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 37/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.21 sec +test 47 + Start 47: graphmolSGroupCatch + +47: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch +47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +45: [02:43:34] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +45: [02:43:34] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +45: [02:43:34] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +45: [02:43:34] non-ring atom 0 marked aromatic +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: Randomness seeded to: 1087283128 +47: =============================================================================== +47: All tests passed (136 assertions in 8 test cases) +47: + 38/230 Test #47: graphmolSGroupCatch .................... Passed 0.11 sec +test 48 + Start 48: graphmolAdjustQueryCatch + +48: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +48: Randomness seeded to: 2025451296 +48: =============================================================================== +48: All tests passed (281 assertions in 10 test cases) +48: + 39/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.24 sec +test 49 + Start 49: chiralityTestsCatch + +49: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch +49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +45: [02:43:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [02:43:34] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: [02:43:34] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: =============================================================================== +45: All tests passed (4464 assertions in 106 test cases) +45: + 40/230 Test #45: graphmolTestsCatch ..................... Passed 0.82 sec +test 50 + Start 50: canonTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 +49: Randomness seeded to: 2997052090 +49: [02:43:34] unable to set wavy bonds for double bonds: 3 +49: [02:43:34] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: [02:43:34] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +34: [02:43:34] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +49: [02:43:34] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: [02:43:34] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: [02:43:34] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +49: =============================================================================== +49: All tests passed (2267 assertions in 79 test cases) +49: + 41/230 Test #49: chiralityTestsCatch .................... Passed 0.45 sec +test 51 + Start 51: moliteratorTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +3: dynamic RDAny:0.747469 s +3: static RDValue:1e-06 s +51: Randomness seeded to: 1516097531 +51: =============================================================================== +51: All tests passed (14 assertions in 4 test cases) +51: + 42/230 Test #51: moliteratorTestsCatch .................. Passed 0.09 sec +test 52 + Start 52: queryTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/queryTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +52: Randomness seeded to: 2927862383 +52: =============================================================================== +52: All tests passed (10 assertions in 1 test case) +52: + 43/230 Test #52: queryTestsCatch ........................ Passed 0.08 sec +test 53 + Start 53: molbundleTestsCatch + +53: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molbundleTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 +3: dynamic RDValue:0.082583 s +3: deleted! +3: [02:43:35] ------------------------------------- +3: [02:43:35] Testing String Pickle Roundtrips. +3: [02:43:35] done +3: [02:43:35] ------------------------------------- +3: [02:43:35] Testing conversion of vect to string. +3: [02:43:35] done +3: [02:43:35] ------------------------------------- +3: [02:43:35] Testing returning const references. +3: [02:43:35] any cast +3: [02:43:35] done: 0.004784 300000 +3: [02:43:35] copy +3: [02:43:35] done: 0.004619 300000 +3: [02:43:35] ref +3: [02:43:35] done: 0.004711 300000 +3: [02:43:35] dict +3: [02:43:35] done: 0.007502 300000 +3: [02:43:35] ref with hasVal +3: [02:43:35] done: 0.006222 300000 +3: [02:43:35] done +3: [02:43:35] ------------------------------------- +3: [02:43:35] Testing dict update. +3: [02:43:35] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 44/230 Test #3: testDict ............................... Passed 3.42 sec +test 54 + Start 54: pickleTestsCatch + +54: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/pickleTestsCatch +54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +54: Test timeout computed to be: 1500 +53: Randomness seeded to: 3621035797 +53: =============================================================================== +53: All tests passed (6 assertions in 1 test case) +53: + 45/230 Test #53: molbundleTestsCatch .................... Passed 0.12 sec +test 55 + Start 55: tableTestsCatch + +55: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/tableTestsCatch +55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +55: Test timeout computed to be: 1500 +55: Randomness seeded to: 868837068 +55: =============================================================================== +55: All tests passed (7 assertions in 2 test cases) +55: +54: Randomness seeded to: 1689825023 +54: =============================================================================== +54: All tests passed (45 assertions in 4 test cases) +54: + 46/230 Test #54: pickleTestsCatch ....................... Passed 0.13 sec + 47/230 Test #55: tableTestsCatch ........................ Passed 0.11 sec +test 56 + Start 56: molopsTestsCatch + +56: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/molopsTestsCatch +56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol +56: Test timeout computed to be: 1500 +test 57 + Start 57: smiTest1 + +57: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +57: Test timeout computed to be: 1500 +56: Randomness seeded to: 717208540 +56: =============================================================================== +56: All tests passed (72 assertions in 4 test cases) +56: + 48/230 Test #56: molopsTestsCatch ....................... Passed 0.10 sec +test 58 + Start 58: smiTest2 + +58: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +58: Test timeout computed to be: 1500 +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [02:43:35] SMILES Parse Error: syntax error while parsing: - +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [02:43:35] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +58: [02:43:35] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 49/230 Test #58: smiTest2 ............................... Passed 0.05 sec +test 59 + Start 59: cxsmilesTest + +59: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +59: Test timeout computed to be: 1500 +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] WARNING: not removing hydrogen atom without neighbors +57: [02:43:35] Invalid chiral specification on atom 0 +57: [02:43:35] Invalid chiral specification on atom 0 +57: [02:43:35] Invalid chiral specification on atom 0 +57: [02:43:35] Invalid chiral specification on atom 0 +57: [02:43:35] Invalid chiral specification on atom 0 +57: [02:43:35] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +57: [02:43:35] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +59: Randomness seeded to: 503119147 59: Test 59: 59: ShortAtropisomerNoCoords.cxsmi @@ -18942,307 +19255,286 @@ 59: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/test_data/ 59: ShortAtropisomerNoCoords.cxsmi 59: -36: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -36: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -36: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -36: smi match: N#CC(=O)[OH] N#CC(=O)[OH] -36: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O -36: smi match: *N(*)C*=O *N(*)C*=O -63: Randomness seeded to: 2254276599 -63: =============================================================================== -63: All tests passed (14 assertions in 2 test cases) -63: -62: Randomness seeded to: 2688380351 -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -36: smi match: O=*C[OH] O=*C[OH] - 44/230 Test #63: v2smiTestCatch ......................... Passed 0.03 sec -test 66 - Start 66: pyDepictor +34: [02:43:35] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +34: F/C=C/Cl +34: [H]/C(F)=C(/[H])Cl +34: F/C=C/Cl +34: F/C=C/Cl +34: C/C(F)=C(/C)Cl +34: [02:43:35] ----------------------- +34: Testing isRingFused + 50/230 Test #34: graphmolMolOpsTest ..................... Passed 2.74 sec +test 60 + Start 60: smaTest1 -66: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/testDepictor.py" -66: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap -66: Test timeout computed to be: 1500 -36: smi match: *=C*=O *=C*=O -36: smi match: *=CC#N *=CC#N -36: smi match: *C[OH] *C[OH] -36: smi match: ** ** -36: smi match: *C[OH] *C[OH] -61: Randomness seeded to: 2023627375 -61: [06:21:43] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -36: smi match: *C(*)=O *C(*)=O -61: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [06:21:43] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -36: smi match: * * -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -36: smi match: *CC(=O)[OH] *CC(=O)[OH] -36: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -36: smi match: *c *c -36: smi match: CN(C)c CN(C)c -36: smi match: c c -36: smi match: *c *c -49: =============================================================================== -49: All tests passed (2267 assertions in 79 test cases) -49: -36: smi match: *c *c -36: smi match: **:*cF **:*cF -36: smi match: cB([OH])[OH] cB([OH])[OH] -36: smi match: N~N~N N~N~N - 45/230 Test #49: chiralityTestsCatch .................... Passed 0.14 sec -test 67 - Start 67: testMrvToMol +60: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +60: Test timeout computed to be: 1500 +57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +57: smi: ClC1CCCCC1 +57: smi: ClC1CCCCC1 +57: smi: ClC1CCCCC1Br +57: smi: c1ccccc1 +57: smi: c1ccncc1 +57: smi: c1cc[nH]c1 +57: smi: c1cc[nH]c1 +57: smi: c1cc[pH]c1 +57: CbC(aC)aC +57: CaC(bC)aC +57: CbC(bC)aC +57: O.C +57: 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 +57: [02:43:36] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +57: [02:43:36] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +57: [02:43:36] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +57: [02:43:36] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +57: [02:43:36] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [02:43:36] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [02:43:36] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [02:43:36] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [02:43:36] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [02:43:36] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: C=c1s/c2n(c1=O)CCCCCCC\N=2 +57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +57: [02:43:36] SMILES Parse Error: extra close parentheses while parsing: C) +57: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 51/230 Test #57: smiTest1 ............................... Passed 0.76 sec +test 61 + Start 61: smiTestCatch -67: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse -67: Test timeout computed to be: 1500 -36: smi match: *N=N* *N=N* -36: smi match: *CC[OH] *CC[OH] -36: smi match: *CC[OH] *CC[OH] -36: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -36: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -36: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -36: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -61: [06:21:43] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [06:21:43] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -36: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -57: [06:21:43] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -36: smi match: *OC(*)=O *OC(*)=O -36: smi match: *C(=O)[OH] *C(=O)[OH] -36: smi match: O=C[OH] O=C[OH] -36: smi match: *OC(=O)O* *OC(=O)O* -36: smi match: * * -36: smi match: *OC(=O)Cl *OC(=O)Cl -36: smi match: *C#N *C#N -36: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -36: smi match: SS SS -36: smi match: * * -36: smi match: *=* *=* -61: [06:21:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [06:21:43] SMARTS Parse Error: syntax error while parsing: C)foo -61: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -36: smi match: *=* *=* -61: [06:21:43] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -61: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -36: smi match: *=* *=* -36: smi match: *=* *=* -36: smi match: C1CO1 C1CO1 -36: smi match: *OC(*)=O *OC(*)=O -36: smi match: * * -36: smi match: *O*[OH] *O*[OH] -36: smi match: COC(C)(C)O COC(C)(C)O -61: [06:21:43] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -36: smi match: *[OH] *[OH] -36: smi match: ** ** -36: smi match: C=N[NH2] C=N[NH2] -36: smi match: C=NC=O C=NC=O -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -36: smi match: * * -36: smi match: C#NC C#NC -36: smi match: CN=C=O CN=C=O -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -36: smi match: CN=C=S CN=C=S -36: smi match: *OC(*)(*)O* *OC(*)(*)O* -36: smi match: *C(*)=O *C(*)=O -36: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -36: smi match: *~*=O *~*=O -36: smi match: *~*=O *~*=O -36: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -36: smi match: * * -36: smi match: *C#N *C#N -36: smi match: *N(=O)~O *N(=O)~O -36: smi match: N N -36: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -36: smi match: C=NO C=NO -36: smi match: O~O O~O -36: smi match: c[OH] c[OH] -36: smi match: O=P(~[OH])~O O=P(~[OH])~O -36: smi match: CO~P(=O)~O CO~P(=O)~O -36: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -36: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -36: smi match: O=P(~O)~O O=P(~O)~O -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -36: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -36: smi match: C[NH2] C[NH2] -36: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -36: smi match: * * -36: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -36: smi match: CS(C)~O CS(C)~O -36: smi match: CS(C)(~O)~O CS(C)(~O)~O -36: smi match: CS(N)(~O)~O CS(N)(~O)~O -36: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -36: smi match: COS(C)(~O)~O COS(C)(~O)~O -36: smi match: *S(C)(~O)~O *S(C)(~O)~O -36: smi match: CN(C)C CN(C)C -36: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -36: smi match: *C(*)=S *C(*)=S -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [06:21:43] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -36: smi match: *OC(*)=S *OC(*)=S -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -36: smi match: * * -36: smi match: C[SH] C[SH] -36: smi match: c[SH] c[SH] -36: smi match: NC(N)=S NC(N)=S -36: smi match: * * -36: smi match: ***** ***** -36: smi match: NC(N)=O NC(N)=O -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 280. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing sf.net issue 285. -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Github2441: Add RDProps interface to Conformers. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Issue2510: Pickle Confs as double. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing loading pickled mols with conformers -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing conformer reading/writing options -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing property reading options -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing property reading options -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing boost::serialization integration -36: [06:21:43] done -36: [06:21:43] ------------------------------------- -36: [06:21:43] Testing github issue 6036 -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 46/230 Test #36: graphmoltestPickler .................... Passed 0.33 sec -test 68 - Start 68: fileParsersTest1 +61: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +61: Test timeout computed to be: 1500 +59: Test +59: +59: ShortAtropisomer.cxsmi +59: +59: Test +59: +59: ShortAtropisomerArom.cxsmi +59: +59: Test +59: +59: AtropManyChirals.cxsmi +59: +59: Test +59: +59: AtropManyChiralsEnhanced.cxsmi +59: +59: Test +59: +59: AtropManyChiralsEnhanced2.cxsmi +59: +59: Test +59: +59: AtropManyChiralsEnhanced3.cxsmi +59: +59: Test +59: +59: AtropManyChiralsEnhanced4.cxsmi +59: +59: Test +59: +59: BMS-986142_3d_chiral.cxsmi +59: +59: Test +59: +59: BMS-986142_3d.cxsmi +59: +59: Test +59: +59: BMS-986142_atrop1.cxsmi +59: +59: Test +59: +59: BMS-986142_atrop2.cxsmi +59: +59: Test +59: +59: BMS-986142_atrop3.cxsmi +59: +59: Test +59: +59: BMS-986142_atrop4.cxsmi +59: +59: Test +59: +59: BMS-986142_atrop5.cxsmi +59: +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [02:43:36] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +60: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +60: [02:43:36] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +60: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +59: Test +59: +59: BMS-986142_atrop6.cxsmi +59: +59: Test +59: +59: BMS-986142_atropBad1.cxsmi +59: +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [02:43:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +60: [02:43:36] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 + 52/230 Test #60: smaTest1 ............................... Passed 0.49 sec +test 62 + Start 62: nontetrahedralCatch -68: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -1: github 4845 - nan coordinates but no crash -1: RDKit 2D -1: -1: 42 44 0 0 0 0 0 0 0 0999 V2000 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 2 4 2 0 -1: 4 5 1 0 -1: 5 6 3 0 -1: 6 7 1 0 -1: 7 8 2 0 -1: 8 9 1 0 -1: 9 10 3 0 -1: 10 11 1 0 -1: 11 12 2 0 -1: 12 13 1 0 -1: 13 14 3 0 -1: 14 15 1 0 -1: 15 16 2 0 -1: 16 17 1 0 -1: 16 18 1 0 -1: 12 19 1 0 -1: 19 20 2 0 -1: 20 21 1 0 -1: 20 22 1 0 -1: 19 23 1 0 -1: 23 24 3 0 -1: 24 25 1 0 -1: 25 26 1 0 -1: 26 27 2 0 -1: 27 28 2 0 -1: 26 29 1 0 -1: 29 30 3 0 -1: 8 31 1 0 -1: 31 32 2 0 -1: 32 33 1 0 -1: 32 34 1 0 -1: 31 35 1 0 -1: 35 36 3 0 -1: 36 37 1 0 -1: 37 38 2 0 -1: 37 39 1 0 -1: 39 40 2 0 -1: 40 41 1 0 -1: 40 42 1 0 -1: 39 4 1 0 -1: 15 7 1 0 -1: 30 11 1 0 -1: M END -1: -62: [06:21:43] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +62: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +62: Test timeout computed to be: 1500 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: Test +59: +59: BMS-986142_atropBad2.cxsmi +59: +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: Randomness seeded to: 2645678978 +61: [02:43:36] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +61: [02:43:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [02:43:36] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +61: [02:43:36] SMARTS Parse Error: unclosed ring for input: 'C1C' +61: [02:43:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [02:43:36] SMARTS Parse Error: syntax error while parsing: C)foo +61: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +61: [02:43:36] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +61: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +61: [02:43:36] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +62: Randomness seeded to: 3089405327 +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [02:43:36] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 62: =============================================================================== 62: All tests passed (308 assertions in 9 test cases) 62: - 47/230 Test #62: nontetrahedralCatch .................... Passed 0.08 sec -test 69 - Start 69: testAtropisomers + 53/230 Test #62: nontetrahedralCatch .................... Passed 0.24 sec +test 63 + Start 63: v2smiTestCatch -69: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +61: [02:43:36] w block attempts to set wedging on bond 0 more than once. +61: [02:43:36] improperly formatted w block +61: [02:43:36] atom 3 is not associated with bond 1(1-2) in w block +59: Test +59: +59: JDQ443_3d.cxsmi +59: +59: Test +59: +59: JDQ443_atrop1.cxsmi +59: +59: Test +59: +59: JDQ443_atrop2.cxsmi +59: +59: Test +59: +59: JDQ443_atrop3.cxsmi +59: +59: Test +59: +59: JDQ443_atrop4.cxsmi +59: +59: Test +59: +59: JDQ443_atropBad1.cxsmi +59: +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [02:43:36] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [02:43:36] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [02:43:36] SMARTS Parse Error: syntax error while parsing: C1C)foo +61: [02:43:36] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +61: [02:43:36] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +61: [02:43:36] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +63: Randomness seeded to: 283394167 +63: =============================================================================== +63: All tests passed (14 assertions in 2 test cases) +63: +61: =============================================================================== +61: All tests passed (1570 assertions in 66 test cases) +61: + 54/230 Test #63: v2smiTestCatch ......................... Passed 0.10 sec +test 64 + Start 64: testDepictor + +64: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor +64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor +64: Test timeout computed to be: 1500 + 55/230 Test #61: smiTestCatch ........................... Passed 0.47 sec +test 65 + Start 65: depictorCatch + +65: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch +65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +59: Test +59: +59: RP-6306_atrop1.cxsmi +59: +59: Test +59: +59: RP-6306_atrop2.cxsmi +59: +59: Test +59: +59: RP-6306_atrop3.cxsmi +59: +59: Test +59: +59: RP-6306_atrop4.cxsmi +59: +59: Test +59: +59: RP-6306_atrop5.cxsmi +59: +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 64: 64: RDKit 2D 64: @@ -19289,60 +19581,157 @@ 64: 8 3 1 0 64: M END 64: -26: done - 48/230 Test #26: testUFFForceField ...................... Passed 0.37 sec -test 70 - Start 70: testSquiggleDoubleBonds - -70: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -69: [06:21:43] ---- Running with POSIX locale ----- - 49/230 Test #1: testCoordGen ........................... Passed 0.46 sec -test 71 - Start 71: testMolSupplier +59: Test +59: +59: RP-6306_atrop6.cxsmi +59: +59: Test +59: +59: RP-6306_atropBad1.cxsmi +59: +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: Test +59: +59: RP-6306_atropBad2.cxsmi +59: +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: Test +59: +59: RP-6306_3d.cxsmi +59: +59: Test +59: +59: Sotorasib_atrop1.cxsmi +59: +59: Test +59: +59: Sotorasib_atrop2.cxsmi +59: +59: Test +59: +59: Sotorasib_atrop3.cxsmi +59: +59: Test +59: +59: Sotorasib_atrop4.cxsmi +59: +59: Test +59: +59: Sotorasib_atrop5.cxsmi +59: +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: Test +59: +59: Sotorasib_atropBad1.cxsmi +59: +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: Test +59: +59: Sotorasib_atropBad2.cxsmi +59: +59: [02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +65: Randomness seeded to: 3863061264 +65: =============================================================================== +65: All tests passed (577 assertions in 17 test cases) +65: + 56/230 Test #65: depictorCatch .......................... Passed 0.62 sec +test 66 + Start 66: pyDepictor -71: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -39: [06:21:43] sorting (hanoi sort) vectors -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: Randomness seeded to: 1864333245 -70: =============================================================================== -70: All tests passed (15 assertions in 3 test cases) -70: -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 50/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.04 sec -test 72 - Start 72: testGeneralFileReader +66: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/testDepictor.py" +66: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap +66: Test timeout computed to be: 1500 +59: Test +59: +59: Sotorasib_3d.cxsmi +59: +59: Test +59: +59: ZM374979_atrop1.cxsmi +59: +59: Test +59: +59: ZM374979_atrop2.cxsmi +59: +59: Test +59: +59: ZM374979_atrop3.cxsmi +59: +59: Test +59: +59: ZM374979_atrop4.cxsmi +59: +59: Test +59: +59: ZM374979_atropBad1.cxsmi +59: +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +64: [02:43:37] Warning: stereochemistry around double bond may be incorrect in depiction. + 57/230 Test #64: testDepictor ........................... Passed 0.95 sec +test 67 + Start 67: testMrvToMol -72: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -68: *************************************** -68: *************************************** -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [06:21:43] -71: ----------------------------------------- -61: [06:21:43] w block attempts to set wedging on bond 0 more than once. -61: [06:21:43] improperly formatted w block -72: [06:21:43] -72: ----------------------------------------- -72: [06:21:43] Finished: testDetermineFormat() -72: [06:21:43] ----------------------------------------- -72: -72: [06:21:43] -72: ----------------------------------------- -61: [06:21:43] atom 3 is not associated with bond 1(1-2) in w block -60: [06:21:43] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -60: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -60: [06:21:43] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -60: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +67: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse +67: Test timeout computed to be: 1500 +59: Test +59: +59: Mrtx1719_3d.cxsmi +59: +59: Test +59: +59: Mrtx1719_atrop1.cxsmi +59: +59: Test +59: +59: Mrtx1719_atrop2.cxsmi +59: +59: Test +59: +59: Mrtx1719_atrop3.cxsmi +59: +59: Test +59: +59: Mrtx1719_atrop4.cxsmi +59: +59: Test +59: +59: Mrtx1719_atropBad1.cxsmi +59: +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 67: Using new chirality perception 67: Test 67: @@ -19380,46 +19769,841 @@ 67: 67: ProblemShort.mol 67: -67: [06:21:43] For a MultipleSgroup expansion, the matching orphaned bond was not found +67: [02:43:37] For a MultipleSgroup expansion, the matching orphaned bond was not found 67: The multiple sgroup will be ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -60: [06:21:43] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -60: [06:21:43] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [06:21:43] bond with order 0 found on line 7. This is not part of the MDL specification. -45: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: Test -59: -59: ShortAtropisomer.cxsmi -59: -59: Test -59: -59: ShortAtropisomerArom.cxsmi -59: -59: Test -59: -59: AtropManyChirals.cxsmi -59: -59: Test -59: -59: AtropManyChiralsEnhanced.cxsmi -59: + 58/230 Test #66: pyDepictor .............................***Exception: SegFault 0.74 sec + +test 68 + Start 68: fileParsersTest1 + +68: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +68: *************************************** +68: *************************************** +68: [02:43:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [02:43:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [02:43:38] bond with order 0 found on line 7. This is not part of the MDL specification. +68: [02:43:38] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [02:43:38] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +68: [02:43:38] 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: generating smiles +68: 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 +68: converting back +68: check isomorphism +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +39: [02:43:39] done: 500000 +39: [02:43:39] Done +27: All 191 tests passed +39: [02:43:39] Testing hanoi with a functor. +39: [02:43:39] Done +39: [02:43:39] Testing basic partition refinement. +39: [02:43:39] Done +39: [02:43:39] Testing partition refinement with neighbors. +39: [02:43:39] Done +39: [02:43:39] testing canonicalization via tie breaking. +39: [02:43:39] Done +39: [02:43:39] testing canonicalization using the wrapper. +39: [02:43:39] Done +39: [02:43:39] testing some specific ordering problems +39: [02:43:39] Finished +39: [02:43:39] testing chiral invariants. +39: [02:43:39] Finished +39: [02:43:39] testing unique ranks in w.r.t. renumbering. +39: [02:43:39] Finished +39: [02:43:39] testing mol fragments. +39: [02:43:39] Finished +39: [02:43:39] testing protein round-tripping. +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +67: Test +67: +67: badWedgeError.sdf +67: +67: Test +67: +67: CrossedDoubleBondWithChiralNbr2.sdf +67: +67: Test +67: +67: CrossedDoubleBondWithChiralNbr.sdf +67: +67: Test +67: +67: SimpleWiggleDoubleBond.sdf +67: +67: Test +67: +67: lostStereoAnd.sdf +67: +67: Test +67: +67: DoubleBondChain.sdf +67: +67: Test +67: +67: UnitsError.sdf +67: +67: Test +67: +67: StarAtom.sdf +67: +67: Test +67: +67: nonProprietary.mol +67: +67: Test +67: +67: ChiralTest.sdf +67: +67: Test +67: +67: TestBond1.mol +67: +67: Test +67: +67: Sgroup_MUL_ParentInMiddle.sdf +67: +67: Test +67: +67: BadRxn.rxn +67: +67: Test +67: +67: FalseChiral.mrv +67: +67: Test +67: +67: FalseChiral.mrv +67: +67: Test +67: +67: Cubane.mrv +67: +67: Test +67: +67: NewChiralTest.mrv +67: +67: Test +67: +67: NewChiralTest.mrv +67: +67: Test +67: +67: NewChiralTestNoChiral.mrv +67: +67: Test +67: +67: NewChiralTestNoChiral.mrv +67: +67: Test +67: +67: NewChiralTestAllChiral.mrv +67: +67: Test +67: +67: NewChiralTestAllChiral.mrv +67: +67: Test +67: +67: DataSgroupMissingUnitsDisplayed.mrv +67: +67: Test +67: +67: lostStereoAnd.mrv +67: +67: Test +67: +67: DoubleBondChain.mrv +67: +67: Test +67: +67: WigglyAndCrossed.mrv +67: +67: Test +67: +67: BondTypes.mrv +67: +67: Test +67: +67: EmbeddedSGroupSUP_MUL.mrv +67: +67: Test +67: +67: EmbeddedSgroupCOP_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupDAT_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupMULTICENTER_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupMUL_MUL.mrv +67: +67: Test +67: +67: EmbeddedSgroupMUL_MUL2.mrv +67: +67: Test +67: +67: EmbeddedSgroupMUL_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupSRU_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupSUPEXP_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupSUPEXP_SUP2.mrv +67: +67: Test +67: +67: EmbeddedSgroupSUP_MULTICENTER.mrv +67: +67: Test +67: +67: EmbeddedSgroupSUP_SUP.mrv +67: +67: Test +67: +67: EmbeddedSgroupSUP_SUP2.mrv +67: +67: Test +67: +67: RgroupBad.mrv +67: +67: Test +67: +67: valenceLessThanDrawn.mrv +67: +67: Test +67: +67: data_sgroup_no_fieldname.mrv +67: +67: Test +67: +67: data_sgroup_empty_field_data.mrv +67: +67: Test +67: +67: radical_value.mrv +67: +67: Test +67: +67: emptyOneLineAtomList.mrv +67: +67: Test +67: +67: mrvValence_value.mrv +67: +67: Test +67: +67: ChiralTest2.mrv +67: +67: Test +67: +67: ChiralTest.mrv +67: +67: Test +67: +67: SnCl2.mrv +67: +67: Test +67: +67: SnH2Cl2.mrv +67: +67: Test +67: +67: marvin01.mrv +67: +67: Test +67: +67: marvin02.mrv +67: +67: Test +67: +67: marvin07.mrv +67: +67: Test +67: +67: marvin10.mrv +67: +67: Test +67: +67: marvin06.mrv +67: +67: Test +67: +67: marvin12.mrv +67: +67: Test +67: +67: EmptyMol.mrv +67: +67: Test +67: +67: Sparse.mrv +67: +67: Test +67: +67: Sparse2.mrv +67: +67: Test +67: +67: Sparse3.mrv +67: +67: Test +67: +67: MarvinNoCoords.mrv +67: +67: Test +67: +67: aspirin.mrv +67: +67: Test +67: +67: MarvinStereoGroupsZeros.mrv +67: +67: Test +67: +67: MarvinStereoGroupsAbs.mrv +67: +67: Test +67: +67: triphenylphosphine.mrv +67: +67: Test +67: +67: MarvinOldSuperGroupTest.mrv +67: +67: Test +67: +67: RadicalTests.mrv +67: +67: Test +67: +67: AnyBond.mrv +67: +67: Test +67: +67: cisBenzene.mrv +67: +67: Test +67: +67: DativeBond.mrv +67: +67: Test +67: +67: MultipleSgroup.mrv +67: +67: Test +67: +67: SgroupExpanded.mrv +67: +67: Test +67: +67: SgroupMultAttach.mrv +67: +67: Test +67: +67: MarvinMissingX2.mrv +67: +67: Test +67: +67: MarvinMissingY2.mrv +67: +67: Test +67: +67: DataSgroup.mrv +67: +67: Test +67: +67: MulticenterSgroup.mrv +67: +67: [02:43:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +67: [02:43:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +67: Test +67: +67: GenericSgroup.mrv +67: +67: Test +67: +67: MonomerSgroup.mrv +67: +67: Test +67: +67: modification_sgroup.mrv +67: +67: Test +67: +67: copolymer_sgroup.mrv +67: +67: Test +67: +67: MultipleSgroupParentInMiddleOfAtomBlock.mrv +67: +67: Test +67: +67: EmbeddedSgroups.mrv +67: +67: Test +67: +67: marvin03.mrv +67: +67: Test +67: +67: MarvinBadMissingMolID.mrv +67: +67: [02:43:39] +67: +67: **** +67: Test Assert +67: Expression Failed: +67: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +67: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +67: ---------- +67: Stacktrace: +67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +67: 2# 0x565EF7A1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 3# 0x565FB1D9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 4# 0x565E6B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 5# 0xF72FED43 in /lib/i386-linux-gnu/libc.so.6 +67: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +67: 7# 0x565E6C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: ---------- +67: **** +67: +67: Test +67: +67: MarvinBadMissingAtomID.mrv +67: +67: Expected id, elementType for an atom definition in MRV file +67: Test +67: +67: MarvinBadX2.mrv +67: +67: The values x2 and y2 must be large floats in MRV file +67: Test +67: +67: MarvinBadY2.mrv +67: +67: The values x2 and y2 must be large floats in MRV file +67: Test +67: +67: MarvinBadStereoGroupsAbs.mrv +67: +67: Unrecognized group definition +67: Test +67: +67: MarvinBadElementType.mrv +67: +67: Test +67: +67: MarvinBadMissingBondID.mrv +67: +67: Test +67: +67: MarvinBadMissingBondAtomRefs +67: +67: Test +67: +67: MarvinBadMissingBondOrder.mrv +67: +67: bond must have one of: order, queryType, or convention in MRV File +67: Test +67: +67: MarvinBadMissingSruMolID.mrv +67: +67: Expected a molID in MRV file +67: Test +67: +67: MarvinBadMissingSruID.mrv +67: +67: Test +67: +67: MarvinBadMissingSruRole.mrv +67: +67: Test +67: +67: MarvinBadMissingSruAtomRef.mrv +67: +67: Test +67: +67: MarvinBadMissingSruTitle.mrv +67: +67: Test +67: +67: MarvinBadSruAtomRef.mrv +67: +67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +67: Test +67: +67: MarvinBadSruID.mrv +67: +67: Test +67: +67: MarvinBadSruRole.mrv +67: +67: Test +67: +67: MarvinBadSruAtomRef.mrv +67: +67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +67: Test +67: +67: MarvinBadSruAtomRef.mrv +67: +67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +67: Test +67: +67: MarvinBadSruConnect.mrv +67: +67: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +67: Test +67: +67: MarvinBadSupAttachAtom.mrv +67: +67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +67: Test +67: +67: MarvinBadSupAttachBond.mrv +67: +67: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +67: Test +67: +67: MarvinBadSupAttachOrder.mrv +67: +67: Order for an AttachmentPoint definition must be an integer in MRV file +67: Test +67: +67: MarvinBadSupAttachAtom.mrv +67: +67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +67: Test +67: +67: MarvinBadSupAttachAtom.mrv +67: +67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 7.534s +12: +12: OK +67: Test +67: +67: MarvinBadSupAttachAtom.mrv +67: +67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +67: Test +67: +67: MarvinBadSupMissingAttachBond.mrv +67: +67: No attachment point found for bond to the condensed atom in a superatomSgroup +67: Test +67: +67: MarvinBadSupMissingAttachOrder.mrv +67: +67: Expected atom, order and bond, for an AttachmentPoint definition in MRV file +39: [02:43:39] Finished +39: [02:43:39] testing stability w.r.t. renumbering. + 59/230 Test #12: pyBV ................................... Passed 8.02 sec +test 69 + Start 69: testAtropisomers + +69: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +39: [02:43:39] Finished +39: [02:43:39] testing smiles round-tripping. +69: [02:43:39] ---- Running with POSIX locale ----- +67: Test +67: +67: marvin03.mrv +67: +67: Test +67: +67: Cubane.mrv +67: +67: Test +67: +67: FalseAtropisomer.mrv +67: +67: Test +67: +67: AtropEnhancedStereo.mrv +67: +67: Test +67: +67: AtropManyChirals.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced2.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced3.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced4.mrv +67: +67: Test +67: +67: BMS-986142_3d_chiral.mrv +67: +67: Test +67: +67: BMS-986142_3d.mrv +67: +67: Test +67: +67: BMS-986142_atrop1.mrv +67: +67: Test +67: +67: BMS-986142_atrop2.mrv +67: +67: Test +67: +67: BMS-986142_atrop3.mrv +67: +67: Test +67: +67: BMS-986142_atrop4.mrv +67: +67: Test +67: +67: BMS-986142_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: BMS-986142_atrop6.mrv +67: +67: Test +67: +67: BMS-986142_atrop7.mrv +67: +67: Test +67: +67: BMS-986142_atrop8.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: BMS-986142_atropBad2.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +67: Test +67: +67: JDQ443_3d.mrv +67: +67: Test +67: +67: JDQ443_atrop1.mrv +67: +67: Test +67: +67: JDQ443_atrop2.mrv +67: +67: Test +67: +67: JDQ443_atrop3.mrv +67: +67: Test +67: +67: JDQ443_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: Test +67: +67: RP-6306_atrop1.mrv +67: +67: Test +67: +67: RP-6306_atrop2.mrv +67: +67: Test +67: +67: RP-6306_atrop3.mrv +67: +67: Test +67: +67: RP-6306_atrop4.mrv +67: +67: Test +67: +67: RP-6306_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: Test +67: +67: RP-6306_atropBad1.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: Test +67: +67: RP-6306_atropBad2.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +67: Test +67: +67: RP-6306_3d.mrv +67: +67: Test +67: +67: Sotorasib_atrop1.mrv +67: +67: Test +67: +67: Sotorasib_atrop2.mrv +67: +67: Test +67: +67: Sotorasib_atrop3.mrv +67: +67: Test +67: +67: Sotorasib_atrop4.mrv +67: +67: Test +67: +67: Sotorasib_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +39: [02:43:40] Finished +39: [02:43:40] testing github #1567: Non-canonical result from MolFragmentToSmiles() +39: [02:43:40] Finished +67: Test +67: +67: Sotorasib_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +67: Test +67: +67: Sotorasib_atropBad2.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 + 60/230 Test #39: hanoiTest .............................. Passed 6.68 sec +test 70 + Start 70: testSquiggleDoubleBonds + +70: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: Sotorasib_3d.mrv +67: +67: Test +67: +67: ZM374979_atrop1.mrv +67: +67: Test +67: +67: ZM374979_atrop2.mrv +67: +67: Test +67: +67: ZM374979_atrop3.mrv +67: +67: Test +67: +67: ZM374979_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +67: Test +67: +67: mrtx1719_3d.mrv +67: +67: Test +67: +67: mrtx1719_atrop1.mrv +67: +67: Test +67: +67: mrtx1719_atrop2.mrv +67: +67: Test +67: +67: mrtx1719_atrop3.mrv +67: +67: Test +67: +67: mrtx1719_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: Randomness seeded to: 156398326 +70: =============================================================================== +70: All tests passed (15 assertions in 3 test cases) +70: + 61/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.14 sec +test 71 + Start 71: testMolSupplier + +71: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [02:43:40] +71: ----------------------------------------- 59: Test 59: -59: AtropManyChiralsEnhanced2.cxsmi +59: AtropCanon1.cxsmi 59: 59: Test 59: -59: AtropManyChiralsEnhanced3.cxsmi +59: AtropCanon2.cxsmi 59: 59: Test 59: -59: AtropManyChiralsEnhanced4.cxsmi +59: AtropCanon3.cxsmi 59: 59: Test 59: @@ -19429,274 +20613,2215 @@ 59: 59: BMS-986142_3d.cxsmi 59: -59: Test -59: -59: BMS-986142_atrop1.cxsmi -59: -59: Test -59: -59: BMS-986142_atrop2.cxsmi -59: -59: Test -59: -59: BMS-986142_atrop3.cxsmi -59: -59: Test -59: -59: BMS-986142_atrop4.cxsmi -59: -59: Test -59: -59: BMS-986142_atrop5.cxsmi +59: =============================================================================== +59: test cases: 29 | 28 passed | 1 failed +59: assertions: 2445 | 2444 passed | 1 failed 59: -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 51/230 Test #60: smaTest1 ............................... Passed 0.18 sec -test 73 - Start 73: testMultithreadedMolSupplier + 62/230 Test #59: cxsmilesTest ...........................***Failed 4.95 sec +Randomness seeded to: 503119147 +Test -73: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [06:21:43] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 P, 7, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 P, 7, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 As, 7, is greater than permitted -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [06:21:43] Explicit valence for atom # 1 As, 7, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [06:21:43] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Bi, 8, is greater than permitted -45: [06:21:43] Explicit valence for atom # 1 Bi, 8, is greater than permitted -45: =============================================================================== -45: All tests passed (4464 assertions in 106 test cases) -45: -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 - 52/230 Test #45: graphmolTestsCatch ..................... Passed 0.35 sec -test 74 - Start 74: testMolWriter + ShortAtropisomerNoCoords.cxsmi -74: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [06:21:43] Finished: testSdf() -72: [06:21:43] ----------------------------------------- -72: -72: [06:21:43] -72: ----------------------------------------- -72: [06:21:43] Finished: testSmi() -72: [06:21:43] ----------------------------------------- -72: -72: [06:21:43] -72: ----------------------------------------- -71: [06:21:43] -71: -71: **** -71: Invariant Violation -71: bad prop value -71: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -71: Failed Expression: nSwaps < 2 -71: ---------- -71: Stacktrace: -71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0xF7EAD591 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x56631CD4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x56603010 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0x56607313 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 7# 0xF748BD43 in /lib/i386-linux-gnu/libc.so.6 -71: 8# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -71: 9# 0x56608EC7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [06:21:43] + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cxsmilesTest is a Catch2 v3.7.1 host application. +Run with -? for options + +------------------------------------------------------------------------------- +testAtropisomersInCXSmiles +------------------------------------------------------------------------------- +./Code/GraphMol/SmilesParse/cxsmiles_test.cpp:1030 +............................................................................... + +./Code/GraphMol/SmilesParse/cxsmiles_test.cpp:818: FAILED: + CHECK( getExpectedValue(expectedFileName) == outMolStr ) +with expansion: + " + RDKit 2D + + 0 0 0 0 0 0 0 0 0 0999 V3000 + M V30 BEGIN CTAB + M V30 COUNTS 14 15 0 0 0 + M V30 BEGIN ATOM + M V30 1 C 3.000000 0.000000 0.000000 0 + M V30 2 C 1.500000 0.000000 0.000000 0 + M V30 3 C 0.750000 -1.299038 0.000000 0 + M V30 4 N 1.500000 -2.598076 0.000000 0 + M V30 5 C 2.991783 -2.754869 0.000000 0 + M V30 6 C 3.303650 -4.222090 0.000000 0 + M V30 7 C 2.004612 -4.972090 0.000000 0 + M V30 8 C 0.889895 -3.968394 0.000000 0 + M V30 9 C -0.577326 -4.280262 0.000000 0 + M V30 10 C -0.750000 -1.299038 0.000000 0 + M V30 11 C -1.500000 -2.598076 0.000000 0 + M V30 12 C -1.500000 0.000000 0.000000 0 + M V30 13 C -0.750000 1.299038 0.000000 0 + M V30 14 C 0.750000 1.299038 0.000000 0 + M V30 END ATOM + M V30 BEGIN BOND + M V30 1 1 1 2 + M V30 2 2 2 3 + M V30 3 1 3 4 + M V30 4 1 4 5 + M V30 5 2 5 6 + M V30 6 1 6 7 + M V30 7 2 7 8 + M V30 8 1 8 9 + M V30 9 1 3 10 CFG=1 + M V30 10 1 10 11 + M V30 11 1 10 12 + M V30 12 1 12 13 + M V30 13 1 13 14 + M V30 14 1 14 2 + M V30 15 1 8 4 + M V30 END BOND + M V30 END CTAB + M END + " + == + " + RDKit 2D + + 0 0 0 0 0 0 0 0 0 0999 V3000 + M V30 BEGIN CTAB + M V30 COUNTS 14 15 0 0 0 + M V30 BEGIN ATOM + M V30 1 C 3.000000 -0.000000 0.000000 0 + M V30 2 C 1.500000 0.000000 0.000000 0 + M V30 3 C 0.750000 -1.299038 0.000000 0 + M V30 4 N 1.500000 -2.598076 0.000000 0 + M V30 5 C 2.991783 -2.754869 0.000000 0 + M V30 6 C 3.303650 -4.222090 0.000000 0 + M V30 7 C 2.004612 -4.972090 0.000000 0 + M V30 8 C 0.889895 -3.968394 0.000000 0 + M V30 9 C -0.577326 -4.280262 0.000000 0 + M V30 10 C -0.750000 -1.299038 0.000000 0 + M V30 11 C -1.500000 -2.598076 0.000000 0 + M V30 12 C -1.500000 0.000000 0.000000 0 + M V30 13 C -0.750000 1.299038 0.000000 0 + M V30 14 C 0.750000 1.299038 0.000000 0 + M V30 END ATOM + M V30 BEGIN BOND + M V30 1 1 1 2 + M V30 2 2 2 3 + M V30 3 1 3 4 + M V30 4 1 4 5 + M V30 5 2 5 6 + M V30 6 1 6 7 + M V30 7 2 7 8 + M V30 8 1 8 9 + M V30 9 1 3 10 CFG=1 + M V30 10 1 10 11 + M V30 11 1 10 12 + M V30 12 1 12 13 + M V30 13 1 13 14 + M V30 14 1 14 2 + M V30 15 1 8 4 + M V30 END BOND + M V30 END CTAB + M END + " +with message: + /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/test_data/ + ShortAtropisomerNoCoords.cxsmi + +Test + + ShortAtropisomer.cxsmi + +Test + + ShortAtropisomerArom.cxsmi + +Test + + AtropManyChirals.cxsmi + +Test + + AtropManyChiralsEnhanced.cxsmi + +Test + + AtropManyChiralsEnhanced2.cxsmi + +Test + + AtropManyChiralsEnhanced3.cxsmi + +Test + + AtropManyChiralsEnhanced4.cxsmi + +Test + + BMS-986142_3d_chiral.cxsmi + +Test + + BMS-986142_3d.cxsmi + +Test + + BMS-986142_atrop1.cxsmi + +Test + + BMS-986142_atrop2.cxsmi + +Test + + BMS-986142_atrop3.cxsmi + +Test + + BMS-986142_atrop4.cxsmi + +Test + + BMS-986142_atrop5.cxsmi + +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + BMS-986142_atrop6.cxsmi + +Test + + BMS-986142_atropBad1.cxsmi + +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +Test + + BMS-986142_atropBad2.cxsmi + +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +Test + + JDQ443_3d.cxsmi + +Test + + JDQ443_atrop1.cxsmi + +Test + + JDQ443_atrop2.cxsmi + +Test + + JDQ443_atrop3.cxsmi + +Test + + JDQ443_atrop4.cxsmi + +Test + + JDQ443_atropBad1.cxsmi + +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +Test + + RP-6306_atrop1.cxsmi + +Test + + RP-6306_atrop2.cxsmi + +Test + + RP-6306_atrop3.cxsmi + +Test + + RP-6306_atrop4.cxsmi + +Test + + RP-6306_atrop5.cxsmi + +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + RP-6306_atrop6.cxsmi + +Test + + RP-6306_atropBad1.cxsmi + +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +[02:43:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +Test + + RP-6306_atropBad2.cxsmi + +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +[02:43:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +Test + + RP-6306_3d.cxsmi + +Test + + Sotorasib_atrop1.cxsmi + +Test + + Sotorasib_atrop2.cxsmi + +Test + + Sotorasib_atrop3.cxsmi + +Test + + Sotorasib_atrop4.cxsmi + +Test + + Sotorasib_atrop5.cxsmi + +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +[02:43:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +Test + + Sotorasib_atropBad1.cxsmi + +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +Test + + Sotorasib_atropBad2.cxsmi + +[02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +[02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +[02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +[02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +[02:43:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +Test + + Sotorasib_3d.cxsmi + +Test + + ZM374979_atrop1.cxsmi + +Test + + ZM374979_atrop2.cxsmi + +Test + + ZM374979_atrop3.cxsmi + +Test + + ZM374979_atrop4.cxsmi + +Test + + ZM374979_atropBad1.cxsmi + +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +Test + + Mrtx1719_3d.cxsmi + +Test + + Mrtx1719_atrop1.cxsmi + +Test + + Mrtx1719_atrop2.cxsmi + +Test + + Mrtx1719_atrop3.cxsmi + +Test + + Mrtx1719_atrop4.cxsmi + +Test + + Mrtx1719_atropBad1.cxsmi + +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +[02:43:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +Test + + AtropCanon1.cxsmi + +Test + + AtropCanon2.cxsmi + +Test + + AtropCanon3.cxsmi + +Test + + BMS-986142_3d_chiral.cxsmi + +Test + + BMS-986142_3d.cxsmi + +=============================================================================== +test cases: 29 | 28 passed | 1 failed +assertions: 2445 | 2444 passed | 1 failed + + +test 72 + Start 72: testGeneralFileReader + +72: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: Test +67: +67: FalseAtropisomer.mrv +67: +67: Test +67: +67: AtropEnhancedStereo.mrv +67: +67: Test +67: +67: AtropManyChirals.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced2.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced3.mrv +67: +67: Test +67: +67: AtropManyChiralsEnhanced4.mrv +67: +67: Test +67: +67: BMS-986142_3d_chiral.mrv +67: +67: Test +67: +67: BMS-986142_3d.mrv +67: +67: Test +67: +67: BMS-986142_atrop1.mrv +67: +67: Test +67: +67: BMS-986142_atrop2.mrv +67: +67: Test +67: +67: BMS-986142_atrop3.mrv +67: +67: Test +67: +67: BMS-986142_atrop4.mrv +67: +67: Test +67: +67: BMS-986142_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +67: Test +67: +67: BMS-986142_atrop6.mrv +67: +67: Test +67: +67: BMS-986142_atrop7.mrv +67: +67: Test +67: +67: BMS-986142_atrop8.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +67: Test +67: +67: BMS-986142_atropBad2.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +72: [02:43:40] +72: ----------------------------------------- +72: [02:43:40] Finished: testDetermineFormat() +72: [02:43:40] ----------------------------------------- +72: +72: [02:43:40] +72: ----------------------------------------- +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:40] +71: +71: **** +71: Invariant Violation +71: bad prop value +71: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +71: Failed Expression: nSwaps < 2 +71: ---------- +71: Stacktrace: +71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0xF7EB3591 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x565F0CD4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x565C2010 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0x565C6313 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 7# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +71: 8# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +71: 9# 0x565C7EC7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: Test +67: +67: JDQ443_3d.mrv +67: +67: Test +67: +67: JDQ443_atrop1.mrv +67: +67: Test +67: +67: JDQ443_atrop2.mrv +67: +67: Test +67: +67: JDQ443_atrop3.mrv +67: +67: Test +67: +67: JDQ443_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +67: Test +67: +67: RP-6306_atrop1.mrv +67: +67: Test +67: +67: RP-6306_atrop2.mrv +67: +67: Test +67: +67: RP-6306_atrop3.mrv +67: +67: Test +67: +67: RP-6306_atrop4.mrv +67: +67: Test +67: +67: RP-6306_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: Test +67: +67: RP-6306_atropBad1.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +67: Test +67: +67: RP-6306_atropBad2.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +72: [02:43:40] Finished: testSdf() +72: [02:43:40] ----------------------------------------- +72: +72: [02:43:40] +72: ----------------------------------------- +72: [02:43:40] Finished: testSmi() +72: [02:43:40] ----------------------------------------- +72: +72: [02:43:40] +72: ----------------------------------------- +67: Test +67: +67: RP-6306_3d.mrv +67: +67: Test +67: +67: Sotorasib_atrop1.mrv +67: +67: Test +67: +67: Sotorasib_atrop2.mrv +67: +67: Test +67: +67: Sotorasib_atrop3.mrv +67: +67: Test +67: +67: Sotorasib_atrop4.mrv +67: +67: Test +67: +67: Sotorasib_atrop5.mrv +67: +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: Sotorasib_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: Sotorasib_atropBad2.mrv +67: +67: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +67: Test +67: +67: Sotorasib_3d.mrv +67: +67: Test +67: +67: ZM374979_atrop1.mrv +67: +67: Test +67: +67: ZM374979_atrop2.mrv +67: +67: Test +67: +67: ZM374979_atrop3.mrv +67: +67: Test +67: +67: ZM374979_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:40] Finished: testMolSup() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:40] Finished: testRandMolSup() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +67: Test +67: +67: mrtx1719_3d.mrv +67: +67: Test +67: +67: mrtx1719_atrop1.mrv +67: +67: Test +67: +67: mrtx1719_atrop2.mrv +67: +67: Test +67: +67: mrtx1719_atrop3.mrv +67: +67: Test +67: +67: mrtx1719_atropBad1.mrv +67: +67: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +72: [02:43:40] Finished: testMae() +72: [02:43:40] ----------------------------------------- +72: +72: [02:43:40] +72: ----------------------------------------- +72: [02:43:40] Finished: testTdt() +72: [02:43:40] ----------------------------------------- +72: +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 + 63/230 Test #72: testGeneralFileReader .................. Passed 0.43 sec +test 73 + Start 73: testMultithreadedMolSupplier + +73: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +67: Test +67: +67: AlexRxn.mrv +67: +67: Test +67: +67: BadReactionSign.mrv +67: +67: Test +67: +67: bondArray_node.mrv +67: +67: Test +67: +67: marvin03.mrv +67: +67: Test +67: +67: marvin04.mrv +67: +67: Test +67: +67: marvin08.mrv +67: +67: Test +67: +67: marvin09.mrv +67: +67: Test +67: +67: marvin11.mrv +67: +67: Test +67: +67: marvin05.mrv +67: +67: Test +67: +67: EmptyRxn.mrv +67: +67: [02:43:40] initialization failed +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [02:43:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:40] Finished: testSmilesSup() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +71: [02:43:40] ------------------------------------------------------ +71: [02:43:40] SMILES Parse Error: syntax error while parsing: fail +71: [02:43:40] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +71: [02:43:40] ERROR: Smiles parse error on line 3 +71: [02:43:40] ERROR: Cannot create molecule from : 'fail' +71: [02:43:40] ------------------------------------------------------ +71: [02:43:40] ------------------------------------------------------ +71: [02:43:40] >>> This may result in an infinite loop. It should finish almost immediately: +71: [02:43:40] <<< done. +71: [02:43:40] Finished: testSmilesSupFromText() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +67: Test +67: +67: RxnNoCoords.mrv +67: +67: Test +67: +67: mrvValenceZero.mrv +67: +67: Test +67: +67: condition_coordinates_mpoint.mrv +67: +67: Test +67: +67: marvin01.mrv +67: +67: Test +67: +67: aspirineSynthesisWithAttributes.mrv +67: +67: Test +67: +67: marvin01.mrv +67: +67: Test +67: +67: NewChiralTest +67: +67: [02:43:40] +67: +67: **** +67: Test Assert +67: Expression Failed: +67: Violation occurred on line 237 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +67: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +67: ---------- +67: Stacktrace: +67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +67: 2# 0x565EA9B9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 3# 0x56600B0B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 4# 0x565E6B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 5# 0xF72FED43 in /lib/i386-linux-gnu/libc.so.6 +67: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +67: 7# 0x565E6C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: ---------- +67: **** +67: +67: terminate called after throwing an instance of 'Invar::Invariant' +67: what(): Expression Failed: + 64/230 Test #67: testMrvToMol ...........................Subprocess aborted***Exception: 3.37 sec +Using new chirality perception +Test + + rxnStereoMarkedCrossed.mrv + +Test + + NewChiralTest.sdf + +Test + + NewChiralTest.sdf + +Test + + NewChiralTestNoChiral.sdf + +Test + + NewChiralTestNoChiral.sdf + +Test + + NewChiralTestAllChiral.sdf + +Test + + NewChiralTestAllChiral.sdf + +Test + + vendor839.sdf + +Test + + ProblemShort.mol + +[02:43:37] For a MultipleSgroup expansion, the matching orphaned bond was not found +The multiple sgroup will be ignored +Test + + badWedgeError.sdf + +Test + + CrossedDoubleBondWithChiralNbr2.sdf + +Test + + CrossedDoubleBondWithChiralNbr.sdf + +Test + + SimpleWiggleDoubleBond.sdf + +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 + + BadRxn.rxn + +Test + + FalseChiral.mrv + +Test + + FalseChiral.mrv + +Test + + Cubane.mrv + +Test + + NewChiralTest.mrv + +Test + + NewChiralTest.mrv + +Test + + NewChiralTestNoChiral.mrv + +Test + + NewChiralTestNoChiral.mrv + +Test + + NewChiralTestAllChiral.mrv + +Test + + NewChiralTestAllChiral.mrv + +Test + + DataSgroupMissingUnitsDisplayed.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 + +[02:43:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +[02:43:39] 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 + +[02:43:39] + +**** +Test Assert +Expression Failed: +Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +---------- +Stacktrace: + 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 2# 0x565EF7A1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 3# 0x565FB1D9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 4# 0x565E6B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 5# 0xF72FED43 in /lib/i386-linux-gnu/libc.so.6 + 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 + 7# 0x565E6C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +---------- +**** + +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 + + Cubane.mrv + +Test + + FalseAtropisomer.mrv + +Test + + AtropEnhancedStereo.mrv + +Test + + AtropManyChirals.mrv + +Test + + AtropManyChiralsEnhanced.mrv + +Test + + AtropManyChiralsEnhanced2.mrv + +Test + + AtropManyChiralsEnhanced3.mrv + +Test + + AtropManyChiralsEnhanced4.mrv + +Test + + BMS-986142_3d_chiral.mrv + +Test + + BMS-986142_3d.mrv + +Test + + BMS-986142_atrop1.mrv + +Test + + BMS-986142_atrop2.mrv + +Test + + BMS-986142_atrop3.mrv + +Test + + BMS-986142_atrop4.mrv + +Test + + BMS-986142_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + BMS-986142_atrop6.mrv + +Test + + BMS-986142_atrop7.mrv + +Test + + BMS-986142_atrop8.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + BMS-986142_atropBad2.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +Test + + JDQ443_3d.mrv + +Test + + JDQ443_atrop1.mrv + +Test + + JDQ443_atrop2.mrv + +Test + + JDQ443_atrop3.mrv + +Test + + JDQ443_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +Test + + RP-6306_atrop1.mrv + +Test + + RP-6306_atrop2.mrv + +Test + + RP-6306_atrop3.mrv + +Test + + RP-6306_atrop4.mrv + +Test + + RP-6306_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +Test + + RP-6306_atropBad1.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +Test + + RP-6306_atropBad2.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +Test + + RP-6306_3d.mrv + +Test + + Sotorasib_atrop1.mrv + +Test + + Sotorasib_atrop2.mrv + +Test + + Sotorasib_atrop3.mrv + +Test + + Sotorasib_atrop4.mrv + +Test + + Sotorasib_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + Sotorasib_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +Test + + Sotorasib_atropBad2.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +Test + + Sotorasib_3d.mrv + +Test + + ZM374979_atrop1.mrv + +Test + + ZM374979_atrop2.mrv + +Test + + ZM374979_atrop3.mrv + +Test + + ZM374979_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +Test + + mrtx1719_3d.mrv + +Test + + mrtx1719_atrop1.mrv + +Test + + mrtx1719_atrop2.mrv + +Test + + mrtx1719_atrop3.mrv + +Test + + mrtx1719_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +Test + + FalseAtropisomer.mrv + +Test + + AtropEnhancedStereo.mrv + +Test + + AtropManyChirals.mrv + +Test + + AtropManyChiralsEnhanced.mrv + +Test + + AtropManyChiralsEnhanced2.mrv + +Test + + AtropManyChiralsEnhanced3.mrv + +Test + + AtropManyChiralsEnhanced4.mrv + +Test + + BMS-986142_3d_chiral.mrv + +Test + + BMS-986142_3d.mrv + +Test + + BMS-986142_atrop1.mrv + +Test + + BMS-986142_atrop2.mrv + +Test + + BMS-986142_atrop3.mrv + +Test + + BMS-986142_atrop4.mrv + +Test + + BMS-986142_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + BMS-986142_atrop6.mrv + +Test + + BMS-986142_atrop7.mrv + +Test + + BMS-986142_atrop8.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + BMS-986142_atropBad2.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +Test + + JDQ443_3d.mrv + +Test + + JDQ443_atrop1.mrv + +Test + + JDQ443_atrop2.mrv + +Test + + JDQ443_atrop3.mrv + +Test + + JDQ443_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +Test + + RP-6306_atrop1.mrv + +Test + + RP-6306_atrop2.mrv + +Test + + RP-6306_atrop3.mrv + +Test + + RP-6306_atrop4.mrv + +Test + + RP-6306_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +Test + + RP-6306_atropBad1.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +Test + + RP-6306_atropBad2.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +Test + + RP-6306_3d.mrv + +Test + + Sotorasib_atrop1.mrv + +Test + + Sotorasib_atrop2.mrv + +Test + + Sotorasib_atrop3.mrv + +Test + + Sotorasib_atrop4.mrv + +Test + + Sotorasib_atrop5.mrv + +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +[02:43:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +Test + + Sotorasib_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +Test + + Sotorasib_atropBad2.mrv + +[02:43:40] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +Test + + Sotorasib_3d.mrv + +Test + + ZM374979_atrop1.mrv + +Test + + ZM374979_atrop2.mrv + +Test + + ZM374979_atrop3.mrv + +Test + + ZM374979_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +Test + + mrtx1719_3d.mrv + +Test + + mrtx1719_atrop1.mrv + +Test + + mrtx1719_atrop2.mrv + +Test + + mrtx1719_atrop3.mrv + +Test + + mrtx1719_atropBad1.mrv + +[02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +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 + +[02:43:40] initialization failed +Test + + RxnNoCoords.mrv + +Test + + mrvValenceZero.mrv + +Test + + condition_coordinates_mpoint.mrv + +Test + + marvin01.mrv + +Test + + aspirineSynthesisWithAttributes.mrv + +Test + + marvin01.mrv + +Test + + NewChiralTest + +[02:43:40] + +**** +Test Assert +Expression Failed: +Violation occurred on line 237 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +---------- +Stacktrace: + 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 2# 0x565EA9B9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 3# 0x56600B0B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 4# 0x565E6B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol + 5# 0xF72FED43 in /lib/i386-linux-gnu/libc.so.6 + 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 + 7# 0x565E6C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +---------- +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + +test 74 + Start 74: testMolWriter + +74: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +71: [02:43:40] Finished: testSmilesWriter() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +73: [02:43:40] 73: ----------------------------------------- -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [06:21:43] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [06:21:43] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [06:21:43] SMARTS Parse Error: syntax error while parsing: C1C)foo -61: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -61: [06:21:43] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -61: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -57: smi: ClC1CCCCC1 -57: smi: ClC1CCCCC1 -57: smi: ClC1CCCCC1Br -57: smi: c1ccccc1 -57: smi: c1ccncc1 -57: smi: c1cc[nH]c1 -57: smi: c1cc[nH]c1 -57: smi: c1cc[pH]c1 -68: [06:21:43] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [06:21:43] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [06:21:43] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -59: Test -59: -59: BMS-986142_atrop6.cxsmi -59: -59: Test -59: -59: BMS-986142_atropBad1.cxsmi -59: -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: =============================================================================== -61: All tests passed (1570 assertions in 66 test cases) -61: -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -57: CbC(aC)aC -57: CaC(bC)aC -57: CbC(bC)aC -57: O.C - 53/230 Test #61: smiTestCatch ........................... Passed 0.20 sec +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [02:43:40] Finished: testSDWriter() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +69: [02:43:40] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [02:43:40] Finished: testSDSupplierEnding() +71: [02:43:40] ----------------------------------------- +71: +71: [02:43:40] ----------------------------------------- +71: [02:43:41] Finished: testSuppliersEmptyFile() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testCisTrans() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testStereoRound() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [02:43:41] Finished: testIssue226() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testTDTSupplier1() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testTDTSupplier2() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testTDTSupplier3() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testSDSupplierFromText() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Spurious data before the first property will be ignored +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Finished: testSDSupplierStrLax1() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Finished: testSDSupplierStrLax2() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Spurious data before the first property will be ignored +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Finished: testSDSupplierFromTextStrLax1() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] ERROR: Problems encountered parsing data fields +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Property will be truncated after the first blank line +71: [02:43:41] Finished: testSDSupplierFromTextStrLax2() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testIssue265() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] ERROR: End of data field name not found +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Explicit valence for atom # 0 F, 2, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule ending on line 16 +71: [02:43:41] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +71: [02:43:41] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] ERROR: Bond line too short: 'M END' on line 18 +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Finished: testSDErrorHandling() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testIssue381() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testSetStreamIndices() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testMixIterAndRandom() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: build: +71: [02:43:41] Finished: testRemoveHs() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +68: [02:43:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +71: [02:43:41] Finished: testGetItemText() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +68: [02:43:41] deprecated group abbreviation ignored on line 24 +71: [02:43:41] Finished: testForwardSDSupplier() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testMissingCRSDSupplier() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testIssue3482695() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +71: [02:43:41] ERROR: Cannot convert 'foo' to unsigned int on line 557 +71: [02:43:41] ERROR: moving to the beginning of the next molecule +68: [02:43:41] +68: +68: **** +68: Post-condition Violation +68: Element 'Mv' not found +68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +68: Failed Expression: anum > -1 +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0xF7DCDCC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0xF7DD75D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 7# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 8# 0x56605F80 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 9# 0x56678E79 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x565EAC18 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +68: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +68: 13# 0x565EADB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +71: [02:43:41] Finished: testIssue3525673() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testBlankLinesInProps() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testSkipLines() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testGitHub23() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testGitHub88() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testGitHub2285() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +71: [02:43:41] ERROR: Smiles parse error on line 1 +71: [02:43:41] ERROR: Cannot create molecule from : 'c1ccccc' +71: [02:43:41] SMILES Parse Error: extra open parentheses for input: 'C(C' +71: [02:43:41] ERROR: Smiles parse error on line 3 +71: [02:43:41] ERROR: Cannot create molecule from : 'C(C' +71: [02:43:41] Explicit valence for atom # 1 C, 5, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule on line 5 +71: [02:43:41] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +71: [02:43:41] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule ending on line 21 +71: [02:43:41] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule ending on line 21 +71: [02:43:41] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule ending on line 21 +71: [02:43:41] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Atom line too short: ' -9.6' on line 28 +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Could not sanitize molecule ending on line 21 +71: [02:43:41] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [02:43:41] ERROR: Atom line too short: ' -9.6' on line 28 +71: [02:43:41] ERROR: moving to the beginning of the next molecule +71: [02:43:41] Finished: testGitHub2479() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] +71: +71: **** +71: Invariant Violation +71: bad chiral bond +71: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +71: Failed Expression: bnd +71: ---------- +71: Stacktrace: +71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0xF7EB3BC4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x565C8DC2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x565C7C63 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +71: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +71: 8# 0x565C7EC7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: +71: [02:43:41] Finished: testGitHub2881() +71: [02:43:41] ----------------------------------------- +71: +71: [02:43:41] ----------------------------------------- +71: [02:43:41] Finished: testGitHub3517() +71: [02:43:41] ----------------------------------------- +71: + 65/230 Test #71: testMolSupplier ........................ Passed 0.95 sec test 75 Start 75: testTplParser 75: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testTplParser 75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -65: Randomness seeded to: 663318341 -65: =============================================================================== -65: All tests passed (577 assertions in 17 test cases) -65: -57: 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 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -57: [06:21:43] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -57: [06:21:43] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' - 54/230 Test #65: depictorCatch .......................... Passed 0.19 sec + 66/230 Test #75: testTplParser .......................... Passed 0.11 sec test 76 Start 76: testMol2ToMol 76: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 -57: [06:21:43] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -57: [06:21:43] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -59: Test -59: -59: BMS-986142_atropBad2.cxsmi -59: -59: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -68: generating smiles -68: 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 -68: converting back -59: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -57: [06:21:43] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [06:21:43] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [06:21:43] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [06:21:43] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [06:21:43] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [06:21:43] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [06:21:43] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: C=c1s/c2n(c1=O)CCCCCCC\N=2 -57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -59: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -57: [06:21:43] SMILES Parse Error: extra close parentheses while parsing: C) -57: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -59: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 - 55/230 Test #57: smiTest1 ............................... Passed 0.25 sec +74: [02:43:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +74: 0.40201265 0.40201265 +74: -0.13299436 -0.13299436 +74: 1.00000017 1.00000017 +74: 0.8762226 0.8762226 +74: 0.9973909 0.9973909 +74: 1.00000003 1.00000003 +74: 0.36613799 0.36613799 +74: 2.1107185 2.1107185 +74: 0.99999982 0.99999982 +74: 2.48696157 2.48696157 +74: 1.00479935 1.00479935 +74: 0.99999999 0.99999999 +74: 3.03311841 3.03311841 +74: 2.23739955 2.23739955 +74: 1.0000001 1.0000001 +74: 3.00772337 3.00772337 +74: 0.37399294 0.37399294 +74: 2.07713325 2.07713325 +74: 3.0077234 3.0077234 +74: 0.37399312 0.37399312 +74: -0.07713336 -0.07713336 +74: [02:43:41] bond with order 0 found on line 11. This is not part of the MDL specification. +74: [02:43:41] bond with order 0 found on line 16. This is not part of the MDL specification. + 67/230 Test #74: testMolWriter .......................... Passed 0.60 sec test 77 Start 77: testSequence 77: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSequence 77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 -68: check isomorphism -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -59: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 56/230 Test #75: testTplParser .......................... Passed 0.04 sec + 68/230 Test #76: testMol2ToMol .......................... Passed 0.18 sec test 78 Start 78: testExtendedStereoParsing 78: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 - 57/230 Test #76: testMol2ToMol .......................... Passed 0.05 sec -test 79 - Start 79: fileParsersCatchTest - -79: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -72: [06:21:43] Finished: testMae() -72: [06:21:43] ----------------------------------------- -72: -72: [06:21:43] -72: ----------------------------------------- -71: [06:21:43] Finished: testMolSup() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -72: [06:21:43] Finished: testTdt() -72: [06:21:43] ----------------------------------------- -72: - 58/230 Test #72: testGeneralFileReader .................. Passed 0.13 sec -test 80 - Start 80: testPropertyLists - -80: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 77: Sequence: GREG 77: HELM: PEPTIDE1{G.R.E.G}$$$$ 77: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -20395,14 +23520,13 @@ 77: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O -71: [06:21:43] Finished: testRandMolSup() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 69/230 Test #78: testExtendedStereoParsing .............. Passed 0.08 sec +test 79 + Start 79: fileParsersCatchTest + +79: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 77: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 77: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C @@ -20689,110 +23813,45 @@ 77: CONECT 27 28 28 29 77: END 77: -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 - 59/230 Test #77: testSequence ........................... Passed 0.05 sec + 70/230 Test #77: testSequence ........................... Passed 0.17 sec +test 80 + Start 80: testPropertyLists + +80: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 +69: Atropisomers- 1 hits 3 misses +69: Final results: +69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +68: [02:43:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [02:43:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 71/230 Test #69: testAtropisomers ....................... Passed 1.88 sec test 81 Start 81: XYZFileParserCatchTest 81: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers 81: Test timeout computed to be: 1500 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 60/230 Test #78: testExtendedStereoParsing .............. Passed 0.05 sec -test 82 - Start 82: cdxmlParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: Test -59: -59: JDQ443_3d.cxsmi -59: -59: Test -59: -59: JDQ443_atrop1.cxsmi -59: -59: Test -59: -59: JDQ443_atrop2.cxsmi -59: -59: Test -59: -59: JDQ443_atrop3.cxsmi -59: -59: Test -59: -59: JDQ443_atrop4.cxsmi -59: -59: Test -59: -59: JDQ443_atropBad1.cxsmi -59: -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 - 61/230 Test #66: pyDepictor .............................***Exception: SegFault 0.27 sec - -test 83 - Start 83: molfileStereoCatchTest - -83: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -59: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -80: Randomness seeded to: 489436897 -80: =============================================================================== -80: All tests passed (95 assertions in 4 test cases) -80: -81: Randomness seeded to: 2190735082 -81: =============================================================================== -81: All tests passed (100 assertions in 2 test cases) -81: -79: Randomness seeded to: 3218773077 -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [06:21:43] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [06:21:43] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -79: [06:21:43] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [06:21:43] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -79: [06:21:43] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [06:21:43] SGroup 1 is invalid and will be ignored - 62/230 Test #80: testPropertyLists ...................... Passed 0.05 sec - 63/230 Test #81: XYZFileParserCatchTest ................. Passed 0.04 sec -test 84 - Start 84: connectTheDotsTest - -84: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -test 85 - Start 85: v2MolSuppliers - -85: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -79: [06:21:43] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [06:21:43] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [06:21:43] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] SGroup 3 referenced on line 40 not found. -79: [06:21:43] +79: Randomness seeded to: 113468796 +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [02:43:41] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [02:43:41] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +79: [02:43:41] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [02:43:41] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +79: [02:43:41] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [02:43:41] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [02:43:41] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup 3 referenced on line 40 not found. +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -20805,24 +23864,24 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DC39E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D689E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x5662E1B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 7# 0x5666E1B5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 16# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] SGroup 3 referenced on line 40 not found. -79: [06:21:43] +79: [02:43:41] SGroup 3 referenced on line 40 not found. +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -20835,29 +23894,29 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DC39E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D689E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x5662E299 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 7# 0x5666E299 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 16# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] no bonds -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] SGroup line too short: 'M SBV 1 6' on line 42 -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -79: [06:21:43] SGroup 2 is invalid and will be ignored -79: [06:21:43] +79: [02:43:41] no bonds +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup line too short: 'M SBV 1 6' on line 42 +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +79: [02:43:41] SGroup 2 is invalid and will be ignored +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -20871,25 +23930,29 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DC38BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D688BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x5662F085 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x5666F085 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] +79: [02:43:41] 79: 79: **** +80: Randomness seeded to: 1766000137 +80: =============================================================================== +80: All tests passed (95 assertions in 4 test cases) +80: 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -20901,46 +23964,26 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DC38BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D688BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x5662F169 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x5666F169 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] +79: [02:43:41] bookmark not found +79: [02:43:41] 79: 79: **** -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [06:21:43] Finished: testSmilesSup() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ------------------------------------------------------ -71: [06:21:43] SMILES Parse Error: syntax error while parsing: fail -71: [06:21:43] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -71: [06:21:43] ERROR: Smiles parse error on line 3 -71: [06:21:43] ERROR: Cannot create molecule from : 'fail' -71: [06:21:43] ------------------------------------------------------ -71: [06:21:43] ------------------------------------------------------ -71: [06:21:43] >>> This may result in an infinite loop. It should finish almost immediately: -71: [06:21:43] <<< done. -71: [06:21:43] Finished: testSmilesSupFromText() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- 79: Pre-condition Violation 79: bond is not part of the SubstanceGroup 79: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp @@ -20952,25 +23995,25 @@ 79: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DC39E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D689E3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x5662F169 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x5666F169 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bond is not part of the SubstanceGroup -79: [06:21:43] SGroup 2 is invalid and will be ignored -79: [06:21:43] +79: [02:43:41] bond is not part of the SubstanceGroup +79: [02:43:41] SGroup 2 is invalid and will be ignored +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -20984,25 +24027,32 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DC38BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D688BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x5662F575 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x5666F575 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] +79: [02:43:41] 79: 79: **** + 72/230 Test #80: testPropertyLists ...................... Passed 0.14 sec +test 82 + Start 82: cdxmlParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp @@ -21014,27 +24064,27 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DC38BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D688BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x5662F659 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x5666F659 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -79: [06:21:43] SGroup 2 is invalid and will be ignored -79: [06:21:43] WARNING: final character of V3000 array is not ')' -79: [06:21:43] +79: [02:43:41] bookmark not found +79: [02:43:41] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +79: [02:43:41] SGroup 2 is invalid and will be ignored +79: [02:43:41] WARNING: final character of V3000 array is not ')' +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21052,21 +24102,21 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662C895 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666C895 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] WARNING: final character of V3000 array is not ')' -79: [06:21:43] +79: [02:43:41] WARNING: final character of V3000 array is not ')' +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21084,23 +24134,23 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662C979 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666C979 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] WARNING: final character of V3000 array is not ')' -79: [06:21:43] +79: [02:43:41] bookmark not found +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] WARNING: final character of V3000 array is not ')' +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21118,27 +24168,21 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662CD85 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666CD85 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -71: [06:21:43] Finished: testSmilesWriter() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [06:21:43] WARNING: final character of V3000 array is not ')' -79: [06:21:43] +79: [02:43:41] WARNING: final character of V3000 array is not ')' +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21156,22 +24200,22 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662CE69 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666CE69 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] SGroup 1 is invalid and will be ignored -79: [06:21:43] +79: [02:43:41] bookmark not found +79: [02:43:41] SGroup 1 is invalid and will be ignored +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21189,20 +24233,20 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662D275 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666D275 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21220,25 +24264,24 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662D359 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666D359 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] SGroup 2 is invalid and will be ignored -79: [06:21:43] +79: [02:43:41] bookmark not found +79: [02:43:41] SGroup 2 is invalid and will be ignored +79: [02:43:41] 79: 79: **** -69: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp @@ -21254,20 +24297,20 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662D765 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666D765 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] +79: [02:43:41] 79: 79: **** 79: Pre-condition Violation @@ -21285,200 +24328,41 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x5662D849 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x5666D849 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:43] bookmark not found -79: [06:21:43] SGroup 2 is invalid and will be ignored -79: [06:21:43] Explicit valence for atom # 2 O, 3, is greater than permitted -71: [06:21:43] Finished: testSDWriter() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -79: [06:21:43] Explicit valence for atom # 1 O, 3, is greater than permitted -79: [06:21:43] Explicit valence for atom # 1 C, 5, is greater than permitted -71: [06:21:43] Finished: testSDSupplierEnding() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Finished: testSuppliersEmptyFile() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Finished: testCisTrans() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [06:21:43] Finished: testStereoRound() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -83: Randomness seeded to: 1478611591 -83: [06:21:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [06:21:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -71: [06:21:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -83: [06:21:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [06:21:43] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -69: [06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [06:21:43] Finished: testIssue226() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -83: =============================================================================== -83: All tests passed (142 assertions in 6 test cases) -83: -79: [06:21:43] sanitize [06:21:43] UNK: [06:21:43] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -71: [06:21:43] Finished: testTDTSupplier1() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- - 64/230 Test #83: molfileStereoCatchTest ................. Passed 0.05 sec -test 86 - Start 86: v2FileParsersCatchTest - -86: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -84: Randomness seeded to: 3544198457 -84: =============================================================================== -84: All tests passed (8 assertions in 1 test case) -84: -71: [06:21:43] Finished: testTDTSupplier2() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Finished: testTDTSupplier3() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Finished: testSDSupplierFromText() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Spurious data before the first property will be ignored -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Finished: testSDSupplierStrLax1() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Finished: testSDSupplierStrLax2() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Spurious data before the first property will be ignored -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Finished: testSDSupplierFromTextStrLax1() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ERROR: Problems encountered parsing data fields -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Property will be truncated after the first blank line -71: [06:21:43] Finished: testSDSupplierFromTextStrLax2() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] Finished: testIssue265() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -71: [06:21:43] ERROR: End of data field name not found -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Explicit valence for atom # 0 F, 2, is greater than permitted -71: [06:21:43] ERROR: Could not sanitize molecule ending on line 16 -71: [06:21:43] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -71: [06:21:43] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -71: [06:21:43] ERROR: moving to the beginning of the next molecule -82: Randomness seeded to: 402281245 -82: [06:21:43] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: [06:21:43] Explicit valence for atom # 3 N, 4, is greater than permitted -82: [06:21:43] CDXMLParser: failed sanitizing skipping fragment 32 -82: [06:21:43] Bad bond in CDXML skipping fragment 58... -82: [06:21:43] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: [06:21:43] Bad bond in CDXML skipping fragment 58... - 65/230 Test #84: connectTheDotsTest ..................... Passed 0.05 sec -test 87 - Start 87: multithreadedSupplierCatchTest +79: [02:43:41] bookmark not found +79: [02:43:41] SGroup 2 is invalid and will be ignored +79: [02:43:41] Explicit valence for atom # 2 O, 3, is greater than permitted +79: [02:43:41] Explicit valence for atom # 1 O, 3, is greater than permitted +79: [02:43:41] Explicit valence for atom # 1 C, 5, is greater than permitted +81: Randomness seeded to: 2151376644 +81: =============================================================================== +81: All tests passed (100 assertions in 2 test cases) +81: + 73/230 Test #81: XYZFileParserCatchTest ................. Passed 0.12 sec +test 83 + Start 83: molfileStereoCatchTest -87: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -71: [06:21:43] ERROR: Bond line too short: 'M END' on line 18 -71: [06:21:43] ERROR: moving to the beginning of the next molecule -71: [06:21:43] Finished: testSDErrorHandling() -71: [06:21:43] ----------------------------------------- -71: -71: [06:21:43] ----------------------------------------- -85: Randomness seeded to: 3915263550 -85: =============================================================================== -85: All tests passed (12 assertions in 5 test cases) -85: -79: [06:21:44] skipping block at line 7: 'BEGIN ATOM' +83: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +79: [02:43:41] sanitize [02:43:41] UNK: [02:43:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [02:43:42] skipping block at line 7: 'BEGIN ATOM' 79: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 79: END 79: -59: Test -59: -59: RP-6306_atrop1.cxsmi -59: -59: Test -59: -59: RP-6306_atrop2.cxsmi -59: -59: Test -59: -59: RP-6306_atrop3.cxsmi -59: -59: Test -59: -59: RP-6306_atrop4.cxsmi -59: -59: Test -59: -59: RP-6306_atrop5.cxsmi -59: -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 66/230 Test #85: v2MolSuppliers ......................... Passed 0.05 sec -test 88 - Start 88: testSubstructMatch - -88: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct -88: Test timeout computed to be: 1500 -71: [06:21:44] Finished: testIssue381() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21490,21 +24374,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x5661CDB3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 3# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x5665CDB3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21516,21 +24400,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x5661CFB0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 3# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x5665CFB0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21542,21 +24426,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x5661C2D5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 3# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x5665C2D5 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21568,21 +24452,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x5661C6F8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 3# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x5665C6F8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21594,39 +24478,31 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x5661CA06 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 3# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x5665CA06 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -79: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 21 -79: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 20 -79: [06:21:44] BEGIN SGROUP line not found on line 14 -79: [06:21:44] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -79: [06:21:44] END SGROUP line not found on line 14 -79: [06:21:44] END SGROUP line not found on line 14 -79: [06:21:44] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -79: [06:21:44] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -79: [06:21:44] +79: [02:43:42] Found a SCD/SED line with missing/empty SDT specification at line 21 +79: [02:43:42] Found a SCD/SED line with missing/empty SDT specification at line 20 +79: [02:43:42] BEGIN SGROUP line not found on line 14 +79: [02:43:42] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +79: [02:43:42] END SGROUP line not found on line 14 +79: [02:43:42] END SGROUP line not found on line 14 +79: [02:43:42] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +79: [02:43:42] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +79: [02:43:42] 79: 79: **** -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 79: Range Error 79: idx 79: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp @@ -21637,93 +24513,57 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::ROMol::getBondWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -79: 4# 0xF7DC9A53 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D6EA53 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x566643F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x56622AEF in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x566A43F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x56662AEF in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -79: [06:21:44] Multiple ATTCHPT values for atom 2 on line 9 -79: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 12 -71: [06:21:44] Finished: testSetStreamIndices() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -79: [06:21:44] SMARTS Parse Error: syntax error while parsing: [#6;R -79: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -79: [06:21:44] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -79: [06:21:44] Skipping empty SMARTS value for SMARTSQ. -79: [06:21:44] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -79: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 12 -79: [06:21:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -71: [06:21:44] Finished: testMixIterAndRandom() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: build: -71: [06:21:44] Finished: testRemoveHs() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -79: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -88: ----------------- Test 1 -88: Done -88: -88: ----------------- Test 2 -88: Done -88: -88: ----------------- Test 3 -88: Done -88: -88: ----------------- Test 4 -88: Done -88: -88: ----------------- Test 5 -88: Done -88: -88: ----------------- Test 5 QueryRoot -88: Done -88: -88: ----------------- Test 6 (Issue71 related) -88: Done -88: -88: ----------------- Testing serial numbers on recursive queries -88: Done -88: -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test multithreading -88: reading molecules -59: Test -59: -59: RP-6306_atrop6.cxsmi -59: -59: Test -59: -59: RP-6306_atropBad1.cxsmi -59: -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -79: [06:21:44] WARNING: Skipping property bar because the value includes an illegal blank line -79: [06:21:44] WARNING: Skipping property baz because the value includes an illegal blank line -79: [06:21:44] WARNING: Skipping property bletch +79: [02:43:42] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +79: [02:43:42] Multiple ATTCHPT values for atom 2 on line 9 +83: Randomness seeded to: 23445988 +83: [02:43:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [02:43:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [02:43:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [02:43:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: =============================================================================== +83: All tests passed (142 assertions in 6 test cases) +83: +79: [02:43:42] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [02:43:42] SMARTS Parse Error: syntax error while parsing: [#6;R +79: [02:43:42] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +79: [02:43:42] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +79: [02:43:42] Skipping empty SMARTS value for SMARTSQ. +79: [02:43:42] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. + 74/230 Test #83: molfileStereoCatchTest ................. Passed 0.14 sec +test 84 + Start 84: connectTheDotsTest + +84: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +79: [02:43:42] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [02:43:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +79: [02:43:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [02:43:42] WARNING: Skipping property bar because the value includes an illegal blank line +79: [02:43:42] WARNING: Skipping property baz because the value includes an illegal blank line +79: [02:43:42] WARNING: Skipping property bletch 79: nope because the name includes a newline -79: [06:21:44] WARNING: Skipping property bletch +79: [02:43:42] WARNING: Skipping property bletch 79: nope2 because the name includes a newline -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Post-condition Violation @@ -21735,26 +24575,35 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0xF7DB0CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DBBF35 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DBD969 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0xF7D55CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D60F35 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D62969 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x565F2436 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x56632436 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +82: Randomness seeded to: 209965614 +82: [02:43:42] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [02:43:42] Explicit valence for atom # 3 N, 4, is greater than permitted +82: [02:43:42] CDXMLParser: failed sanitizing skipping fragment 32 +82: [02:43:42] Bad bond in CDXML skipping fragment 58... +82: [02:43:42] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [02:43:42] Bad bond in CDXML skipping fragment 58... +68: ---------------------------------- +68: ---------------------------------- +79: [02:43:42] 79: 79: **** 79: Post-condition Violation @@ -21766,26 +24615,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0xF7DB0CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DBBF35 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0xF7DBD969 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0xF7D55CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D60F35 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0xF7D62969 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x565F19CC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 9# 0x566319CC in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 18# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Post-condition Violation @@ -21797,25 +24646,25 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0xF7DB0CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DBA5D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0xF7D55CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D5F5D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x565F23CE in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x566323CE in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Post-condition Violation @@ -21827,62 +24676,48 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0xF7DB0CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0xF7DBA5D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0xF7D55CC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0xF7D5F5D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x565F1FA7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 8# 0x56631FA7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 17# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -71: [06:21:44] Finished: testGetItemText() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -79: [06:21:44] atom 3 has a negative isotope value. line: 15 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -86: Randomness seeded to: 2462747795 -86: =============================================================================== -86: All tests passed (6 assertions in 1 test case) -86: -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 - 67/230 Test #86: v2FileParsersCatchTest ................. Passed 0.04 sec -test 89 - Start 89: substructTestCatch - -89: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct -89: Test timeout computed to be: 1500 -59: Test -59: -59: RP-6306_atropBad2.cxsmi -59: -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -64: [06:21:44] Warning: stereochemistry around double bond may be incorrect in depiction. -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -79: [06:21:44] +68: [02:43:42] +68: +68: **** +68: Pre-condition Violation +68: rlabel out of range for MDL files +68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +68: Failed Expression: rlabel >= 0 && rlabel < 100 +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +68: 3# 0x56615582 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x56678EF1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x565EAC18 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +68: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +68: 8# 0x565EADB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +79: [02:43:42] atom 3 has a negative isotope value. line: 15 +68: [02:43:42] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +79: [02:43:42] 79: 79: **** 79: Invariant Violation @@ -21893,25 +24728,23 @@ 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -79: 2# 0xF7E7E591 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 2# 0xF7E23591 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x56664B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x56634C1D in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 4# 0x566A4B74 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x56674C1D in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 13# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 14# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -82: [06:21:44] WARNING: not removing hydrogen atom without neighbors -82: [06:21:44] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -79: [06:21:44] +79: [02:43:42] 79: 79: **** 79: Pre-condition Violation @@ -21924,327 +24757,282 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x566351C3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x566AD1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x566ADE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x566AE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x5667D4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x5667D832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x565E94A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0xF73D5D43 in /lib/i386-linux-gnu/libc.so.6 +79: 4# 0x566751C3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x566ED1BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x566EDE9F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x566EE504 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x566BD4A4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x566BD832 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x566294A6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0xF736ED43 in /lib/i386-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -79: 13# 0x565E94E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x566294E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -71: [06:21:44] Finished: testForwardSDSupplier() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testMissingCRSDSupplier() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testIssue3482695() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] ERROR: Cannot convert 'foo' to unsigned int on line 557 -71: [06:21:44] ERROR: moving to the beginning of the next molecule -71: [06:21:44] Finished: testIssue3525673() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testBlankLinesInProps() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testSkipLines() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testGitHub23() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testGitHub88() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -82: [06:21:44] Incomplete atom labelling, cannot make bond -82: [06:21:44] Incomplete atom labelling, cannot make bond +84: Randomness seeded to: 3616069526 +84: =============================================================================== +84: All tests passed (8 assertions in 1 test case) +84: + 75/230 Test #84: connectTheDotsTest ..................... Passed 0.12 sec +test 85 + Start 85: v2MolSuppliers + +85: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] WARNING: not removing hydrogen atom without neighbors +82: [02:43:42] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +82: [02:43:42] Incomplete atom labelling, cannot make bond +82: [02:43:42] Incomplete atom labelling, cannot make bond +79: [02:43:42] ERROR: molecules without atoms cannot be exported to Maestro files. +79: [02:43:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +79: [02:43:42] ERROR: the mol cannot be kekulized, and will not be written to the output file. +79: [02:43:42] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +79: [02:43:42] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[02:43:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [02:43:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [02:43:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [02:43:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +85: Randomness seeded to: 581953377 +85: =============================================================================== +85: All tests passed (12 assertions in 5 test cases) +85: + 76/230 Test #85: v2MolSuppliers ......................... Passed 0.13 sec +test 86 + Start 86: v2FileParsersCatchTest + +86: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +82: [02:43:42] Incomplete atom labelling, cannot make bond +86: Randomness seeded to: 2290334343 +86: =============================================================================== +86: All tests passed (6 assertions in 1 test case) +86: + 77/230 Test #86: v2FileParsersCatchTest ................. Passed 0.09 sec +test 87 + Start 87: multithreadedSupplierCatchTest + +87: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 +82: [02:43:42] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [02:43:42] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [02:43:42] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +82: [02:43:42] Failed to parse XML fragment 5 node: b attribute: Order: 5 +82: [02:43:42] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: =============================================================================== +82: All tests passed (263 assertions in 7 test cases) +82: + 78/230 Test #82: cdxmlParserCatchTest ................... Passed 0.61 sec +test 88 + Start 88: testSubstructMatch + +88: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct +88: Test timeout computed to be: 1500 +88: ----------------- Test 1 +88: Done +88: +88: ----------------- Test 2 +88: Done +88: +88: ----------------- Test 3 +88: Done +88: +88: ----------------- Test 4 +88: Done +88: +88: ----------------- Test 5 +88: Done +88: +88: ----------------- Test 5 QueryRoot +88: Done +88: +88: ----------------- Test 6 (Issue71 related) +88: Done +88: +88: ----------------- Testing serial numbers on recursive queries +88: Done +88: +88: [02:43:42] ------------------------------------- +88: [02:43:42] Test multithreading +88: reading molecules 88: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 88: processing 88: launch :0 88: launch :1 88: launch :2 88: launch :3 -71: [06:21:44] Finished: testGitHub2285() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -71: [06:21:44] ERROR: Smiles parse error on line 1 -71: [06:21:44] ERROR: Cannot create molecule from : 'c1ccccc' -71: [06:21:44] SMILES Parse Error: extra open parentheses for input: 'C(C' -71: [06:21:44] ERROR: Smiles parse error on line 3 -71: [06:21:44] ERROR: Cannot create molecule from : 'C(C' -71: [06:21:44] Explicit valence for atom # 1 C, 5, is greater than permitted -71: [06:21:44] ERROR: Could not sanitize molecule on line 5 -71: [06:21:44] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -71: [06:21:44] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Could not sanitize molecule ending on line 21 -71: [06:21:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Could not sanitize molecule ending on line 21 -71: [06:21:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Could not sanitize molecule ending on line 21 -71: [06:21:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Atom line too short: ' -9.6' on line 28 -71: [06:21:44] ERROR: moving to the beginning of the next molecule -71: [06:21:44] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Could not sanitize molecule ending on line 21 -71: [06:21:44] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [06:21:44] ERROR: Atom line too short: ' -9.6' on line 28 -71: [06:21:44] ERROR: moving to the beginning of the next molecule -71: [06:21:44] Finished: testGitHub2479() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] -71: -71: **** -71: Invariant Violation -71: bad chiral bond -71: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -71: Failed Expression: bnd -71: ---------- -71: Stacktrace: -71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0xF7EADBC4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x56609DC2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x56608C63 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0xF748BD43 in /lib/i386-linux-gnu/libc.so.6 -71: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -71: 8# 0x56608EC7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -71: [06:21:44] Finished: testGitHub2881() -71: [06:21:44] ----------------------------------------- -71: -71: [06:21:44] ----------------------------------------- -71: [06:21:44] Finished: testGitHub3517() -71: [06:21:44] ----------------------------------------- -71: - 68/230 Test #71: testMolSupplier ........................ Passed 0.33 sec +68: [02:43:42] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [02:43:42] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +88: done +88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +88: processing2 +88: launch2 :0 +88: launch2 :1 +88: launch2 :2 +88: launch2 :3 +68: [02:43:43] Empty atom list: 'M ALS 1 0 F' on line 8. +88: done +88: preprocessing 3 +88: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +88: processing3 +88: launch3 :0 +88: launch3 :1 +88: launch3 :2 +88: launch3 :3 +68: de_DE.UTF-8 +68: [02:43:43] ------------------------------------- +68: [02:43:43] Test multithreading Locale Switching +68: [02:43:43] Test multithreading (Done) +68: [02:43:43] ------------------------------------- +68: *************************************** +68: *************************************** +68: [02:43:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [02:43:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [02:43:43] bond with order 0 found on line 7. This is not part of the MDL specification. +68: [02:43:43] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [02:43:43] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +68: [02:43:43] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: generating smiles +68: 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 +68: converting back +88: done +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test GitHub issue 15 +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test GitHub issue 409 +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test chiral matching +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +68: check isomorphism +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test dative-bond matching +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test cis/trans matching +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test cis/trans matching part 2 +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +88: [02:43:43] done +88: [02:43:43] ------------------------------------- +88: [02:43:43] Testing matching E/Z against Cis/Trans stereo bonds +88: [02:43:43] +88: +88: **** +88: Pre-condition Violation +88: matches must not be empty +88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +88: Failed Expression: !matches.empty() +88: ---------- +88: Stacktrace: +88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 4# 0x565ABB14 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x565A8EBA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0xF74BED43 in /lib/i386-linux-gnu/libc.so.6 +88: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +88: 8# 0x565A8FF7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: ---------- +88: **** +88: +88: [02:43:43] +88: +88: **** +88: Pre-condition Violation +88: matches must not be empty +88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +88: Failed Expression: !matches.empty() +88: ---------- +88: Stacktrace: +88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 4# 0x5659FD63 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x565A8EBA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0xF74BED43 in /lib/i386-linux-gnu/libc.so.6 +88: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +88: 8# 0x565A8FF7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: ---------- +88: **** +88: +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test substructure matching with a pathological case for symmetric SSSR +88: [02:43:43] ------------------------------------- +88: [02:43:43] Test isAtomTerminalRGroupOrQueryHydrogen + 79/230 Test #88: testSubstructMatch ..................... Passed 1.10 sec +test 89 + Start 89: substructTestCatch + +89: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct +89: Test timeout computed to be: 1500 + 80/230 Test #41: resMolSupplierTest ..................... Passed 10.62 sec test 90 Start 90: testGenericGroups 90: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 90: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GenericGroups 90: Test timeout computed to be: 1500 -82: [06:21:44] Incomplete atom labelling, cannot make bond -79: [06:21:44] ERROR: molecules without atoms cannot be exported to Maestro files. -79: [06:21:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -79: [06:21:44] ERROR: the mol cannot be kekulized, and will not be written to the output file. -79: [06:21:44] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -79: [06:21:44] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[06:21:44] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -79: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [06:21:44] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -79: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -82: [06:21:44] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [06:21:44] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [06:21:44] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -82: [06:21:44] Failed to parse XML fragment 5 node: b attribute: Order: 5 -82: [06:21:44] Invalid or missing fragment id from CDXML fragment, assigning new one... -59: Test -59: -59: RP-6306_3d.cxsmi -59: -59: Test -59: -59: Sotorasib_atrop1.cxsmi -59: -59: Test -59: -59: Sotorasib_atrop2.cxsmi -59: -59: Test -59: -59: Sotorasib_atrop3.cxsmi -59: -59: Test -59: -59: Sotorasib_atrop4.cxsmi -59: -59: Test -59: -59: Sotorasib_atrop5.cxsmi -59: -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -82: =============================================================================== -82: All tests passed (263 assertions in 7 test cases) -82: - 69/230 Test #82: cdxmlParserCatchTest ................... Passed 0.21 sec +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +89: Randomness seeded to: 1081093725 +89: =============================================================================== +89: All tests passed (197 assertions in 9 test cases) +89: + 81/230 Test #89: substructTestCatch ..................... Passed 0.79 sec test 91 Start 91: testReaction 91: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction 91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 91: Test timeout computed to be: 1500 -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -34: [06:21:44] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. - 70/230 Test #64: testDepictor ........................... Passed 0.50 sec -test 92 - Start 92: testReactionFingerprints - -92: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -92: Test timeout computed to be: 1500 -59: Test -59: -59: Sotorasib_atropBad1.cxsmi -59: -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -3: dynamic boost any:0.717579 s -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -74: [06:21:44] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -74: 0.40201265 0.40201265 -74: -0.13299436 -0.13299436 -74: 1.00000017 1.00000017 -74: 0.8762226 0.8762226 -74: 0.9973909 0.9973909 -74: 1.00000003 1.00000003 -74: 0.36613799 0.36613799 -74: 2.1107185 2.1107185 -74: 0.99999982 0.99999982 -74: 2.48696157 2.48696157 -74: 1.00479935 1.00479935 -74: 0.99999999 0.99999999 -74: 3.03311841 3.03311841 -74: 2.23739955 2.23739955 -74: 1.0000001 1.0000001 -74: 3.00772337 3.00772337 -74: 0.37399294 0.37399294 -74: 2.07713325 2.07713325 -74: 3.0077234 3.0077234 -74: 0.37399312 0.37399312 -74: -0.07713336 -0.07713336 -59: Test -59: -59: Sotorasib_atropBad2.cxsmi -59: -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -74: [06:21:44] bond with order 0 found on line 11. This is not part of the MDL specification. -74: [06:21:44] bond with order 0 found on line 16. This is not part of the MDL specification. -92: [06:21:44] ------------------------------------- -92: [06:21:44] Test Reaction StructuralFingerprint +27: All 191 tests passed 91: smi: O=C1CNC(=O)CN1 91: 1: O=C1CNC(=O)CN1 91: 2: COOC -91: [06:21:44] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [06:21:44] 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]' +91: [02:43:44] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [02:43:44] 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]' 91: O=C1CNC(=O)CN1 -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] ------------------------------------- -92: [06:21:44] Test Reaction DifferenceFingerprint -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use AtomPairGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [06:21:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -91: [06:21:44] product atom-mapping number 1 found multiple times. -91: [06:21:44] mapped atoms in the reactants were not mapped in the products. +91: [02:43:44] product atom-mapping number 1 found multiple times. +91: [02:43:44] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 - 71/230 Test #92: testReactionFingerprints ............... Passed 0.05 sec -test 93 - Start 93: testEnumeration - -93: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 - 72/230 Test #74: testMolWriter .......................... Passed 0.38 sec -test 94 - Start 94: rxnTestCatch - -94: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -91: [06:21:44] atom 0 in product 0 has multiple charge specifications. +91: [02:43:44] atom 0 in product 0 has multiple charge specifications. 91: mass: 15.0001 91: Oc1ccccn1 91: Oc1ccc[nH]1 -69: Atropisomers- 1 hits 3 misses -69: Final results: -69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 73/230 Test #69: testAtropisomers ....................... Passed 0.50 sec -test 95 - Start 95: pyChemReactions - -95: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -95: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap -95: Test timeout computed to be: 1500 -3: static RDAny:0.071273 s -91: [06:21:44] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -91: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -91: [06:21:44] SMARTS Parse Error: syntax error while parsing: ([C:2] -91: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -91: [06:21:44] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -91: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -91: [06:21:44] SMARTS Parse Error: syntax error while parsing: [C:2]) -91: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -91: [06:21:44] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [06:21:44] 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]' -88: done -88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -88: processing2 -88: launch2 :0 -88: launch2 :1 -88: launch2 :2 -88: launch2 :3 -91: [06:21:44] +91: [02:43:44] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +91: [02:43:44] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +91: [02:43:44] SMARTS Parse Error: syntax error while parsing: ([C:2] +91: [02:43:44] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +91: [02:43:44] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +91: [02:43:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +91: [02:43:44] SMARTS Parse Error: syntax error while parsing: [C:2]) +91: [02:43:44] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +91: [02:43:44] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [02:43:44] 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]' +91: [02:43:44] 91: 91: **** 91: Test Assert @@ -22255,41 +25043,41 @@ 91: Stacktrace: 91: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 91: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -91: 2# 0x5668FBCD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction -91: 3# 0x565DEE94 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction -91: 4# 0xF735AD43 in /lib/i386-linux-gnu/libc.so.6 +91: 2# 0x5674BBCD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction +91: 3# 0x5669AE94 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction +91: 4# 0xF735ED43 in /lib/i386-linux-gnu/libc.so.6 91: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -91: 6# 0x565DF0E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction +91: 6# 0x5669B0E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction 91: ---------- 91: **** 91: 91: terminate called after throwing an instance of 'Invar::Invariant' 91: what(): Expression Failed: - 74/230 Test #91: testReaction ...........................Subprocess aborted***Exception: 0.10 sec + 82/230 Test #91: testReaction ...........................Subprocess aborted***Exception: 0.27 sec smi: O=C1CNC(=O)CN1 1: O=C1CNC(=O)CN1 2: COOC -[06:21:44] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -[06:21:44] 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]' +[02:43:44] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +[02:43:44] 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]' O=C1CNC(=O)CN1 -[06:21:44] product atom-mapping number 1 found multiple times. -[06:21:44] mapped atoms in the reactants were not mapped in the products. +[02:43:44] product atom-mapping number 1 found multiple times. +[02:43:44] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 4 -[06:21:44] atom 0 in product 0 has multiple charge specifications. +[02:43:44] atom 0 in product 0 has multiple charge specifications. mass: 15.0001 Oc1ccccn1 Oc1ccc[nH]1 -[06:21:44] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -[06:21:44] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -[06:21:44] SMARTS Parse Error: syntax error while parsing: ([C:2] -[06:21:44] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -[06:21:44] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -[06:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -[06:21:44] SMARTS Parse Error: syntax error while parsing: [C:2]) -[06:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -[06:21:44] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -[06:21:44] 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]' -[06:21:44] +[02:43:44] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +[02:43:44] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +[02:43:44] SMARTS Parse Error: syntax error while parsing: ([C:2] +[02:43:44] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +[02:43:44] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +[02:43:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +[02:43:44] SMARTS Parse Error: syntax error while parsing: [C:2]) +[02:43:44] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +[02:43:44] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +[02:43:44] 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]' +[02:43:44] **** Test Assert @@ -22300,735 +25088,234 @@ Stacktrace: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 2# 0x5668FBCD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction - 3# 0x565DEE94 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction - 4# 0xF735AD43 in /lib/i386-linux-gnu/libc.so.6 + 2# 0x5674BBCD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction + 3# 0x5669AE94 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction + 4# 0xF735ED43 in /lib/i386-linux-gnu/libc.so.6 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 - 6# 0x565DF0E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction + 6# 0x5669B0E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction ---------- **** terminate called after throwing an instance of 'Invar::Invariant' what(): Expression Failed: +test 92 + Start 92: testReactionFingerprints + +92: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +92: Test timeout computed to be: 1500 +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +92: [02:43:44] ------------------------------------- +92: [02:43:44] Test Reaction StructuralFingerprint +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] ------------------------------------- +92: [02:43:44] Test Reaction DifferenceFingerprint +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use AtomPairGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [02:43:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 83/230 Test #92: testReactionFingerprints ............... Passed 0.14 sec +test 93 + Start 93: testEnumeration + +93: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +93: 30000000 30000000 +87: Randomness seeded to: 2616860396 +87: [02:43:45] Explicit valence for atom # 9 N, 6, is greater than permitted +68: [02:43:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [02:43:45] deprecated group abbreviation ignored on line 24 +68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +68: [02:43:45] +68: +68: **** +68: Post-condition Violation +68: Element 'Mv' not found +68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +68: Failed Expression: anum > -1 +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0xF7DCDCC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0xF7DD75D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 7# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 8# 0x56605F80 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 9# 0x56678E79 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x565EAC93 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +68: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +68: 13# 0x565EADB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +90: Randomness seeded to: 166501842 +90: =============================================================================== +90: All tests passed (11480 assertions in 38 test cases) +90: + 84/230 Test #90: testGenericGroups ...................... Passed 1.71 sec +test 94 + Start 94: rxnTestCatch + +94: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +94: Randomness seeded to: 3236637415 +94: [02:43:46] atom 0 in product 0 has multiple charge specifications. +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 34 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 36 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 38 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 40 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 42 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 87 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 89 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 91 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 93 +94: [02:43:46] Found a SCD/SED line with missing/empty SDT specification at line 95 +94: [02:43:46] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [02:43:46] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [02:43:46] SMARTS Parse Error: unclosed ring for input: 'CC1' +94: [02:43:46] SMILES Parse Error: unclosed ring for input: 'CC1' +94: [02:43:46] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [02:43:46] product atom-mapping number 2 not found in reactants. +94: [02:43:46] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [02:43:46] product atom-mapping number 2 not found in reactants. +94: [02:43:46] CX Extensions: Substance group hierarchy is not always preserved. +94: [02:43:46] CX Extensions: Substance group hierarchy is not always preserved. +94: [02:43:46] reactant 0 has no mapped atoms. +94: [02:43:46] product 0 has no mapped atoms. +94: [02:43:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [02:43:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [02:43:46] Explicit valence for atom # 1 O, 5, is greater than permitted +94: =============================================================================== +94: All tests passed (702 assertions in 28 test cases) +94: + 85/230 Test #94: rxnTestCatch ........................... Passed 0.21 sec +test 95 + Start 95: pyChemReactions + +95: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +95: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap +95: Test timeout computed to be: 1500 +68: [02:43:46] 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: [02:43:46] 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: ---------------------------------- +68: ---------------------------------- +68: [02:43:46] +68: +68: **** +68: Pre-condition Violation +68: rlabel out of range for MDL files +68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +68: Failed Expression: rlabel >= 0 && rlabel < 100 +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 +68: 3# 0x56615582 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x56678EF1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x565EAC93 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0xF747ED43 in /lib/i386-linux-gnu/libc.so.6 +68: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +68: 8# 0x565EADB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +68: [02:43:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 86/230 Test #95: pyChemReactions ........................***Exception: SegFault 0.44 sec + test 96 Start 96: pyChemReactionEnumerations 96: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 96: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 96: Test timeout computed to be: 1500 -88: done -88: preprocessing 3 -88: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -88: processing3 -88: launch3 :0 -88: launch3 :1 -88: launch3 :2 -88: launch3 :3 -59: Test -59: -59: Sotorasib_3d.cxsmi -59: -59: Test -59: -59: ZM374979_atrop1.cxsmi -59: -59: Test -59: -59: ZM374979_atrop2.cxsmi -59: -59: Test -59: -59: ZM374979_atrop3.cxsmi -59: -59: Test -59: -59: ZM374979_atrop4.cxsmi -59: -59: Test -59: -59: ZM374979_atropBad1.cxsmi -59: -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -94: Randomness seeded to: 1104147478 -94: [06:21:44] atom 0 in product 0 has multiple charge specifications. -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 34 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 36 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 38 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 40 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 42 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 87 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 89 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 91 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 93 -94: [06:21:44] Found a SCD/SED line with missing/empty SDT specification at line 95 -94: [06:21:44] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [06:21:44] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [06:21:44] SMARTS Parse Error: unclosed ring for input: 'CC1' -94: [06:21:44] SMILES Parse Error: unclosed ring for input: 'CC1' -67: Test -67: -67: badWedgeError.sdf -67: -67: Test -67: -67: CrossedDoubleBondWithChiralNbr2.sdf -67: -67: Test -67: -67: CrossedDoubleBondWithChiralNbr.sdf -67: -67: Test -67: -67: SimpleWiggleDoubleBond.sdf -67: -67: Test -67: -67: lostStereoAnd.sdf -67: -67: Test -67: -67: DoubleBondChain.sdf -67: -67: Test -67: -67: UnitsError.sdf -67: -67: Test -67: -67: StarAtom.sdf -67: -67: Test -67: -67: nonProprietary.mol -67: -67: Test -67: -67: ChiralTest.sdf -67: -67: Test -67: -67: TestBond1.mol -67: -67: Test -67: -67: Sgroup_MUL_ParentInMiddle.sdf -67: -67: Test -67: -67: BadRxn.rxn -67: -67: Test -67: -67: FalseChiral.mrv -67: -67: Test -67: -67: FalseChiral.mrv -67: -67: Test -67: -67: Cubane.mrv -67: -67: Test -67: -67: NewChiralTest.mrv -67: -67: Test -67: -67: NewChiralTest.mrv -67: -67: Test -67: -67: NewChiralTestNoChiral.mrv -67: -67: Test -67: -67: NewChiralTestNoChiral.mrv -67: -67: Test -67: -67: NewChiralTestAllChiral.mrv -67: -67: Test -67: -67: NewChiralTestAllChiral.mrv -67: -67: Test -67: -67: DataSgroupMissingUnitsDisplayed.mrv -67: -67: Test -67: -67: lostStereoAnd.mrv -67: -67: Test -67: -67: DoubleBondChain.mrv -67: -67: Test -67: -67: WigglyAndCrossed.mrv -67: -67: Test -67: -67: BondTypes.mrv -67: -67: Test -67: -67: EmbeddedSGroupSUP_MUL.mrv -67: -67: Test -67: -67: EmbeddedSgroupCOP_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupDAT_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupMULTICENTER_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupMUL_MUL.mrv -67: -67: Test -67: -67: EmbeddedSgroupMUL_MUL2.mrv -67: -67: Test -67: -67: EmbeddedSgroupMUL_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupSRU_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupSUPEXP_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupSUPEXP_SUP2.mrv -67: -67: Test -67: -67: EmbeddedSgroupSUP_MULTICENTER.mrv -67: -67: Test -67: -67: EmbeddedSgroupSUP_SUP.mrv -67: -67: Test -67: -67: EmbeddedSgroupSUP_SUP2.mrv -67: -67: Test -67: -67: RgroupBad.mrv -67: -67: Test -67: -67: valenceLessThanDrawn.mrv -67: -67: Test -67: -67: data_sgroup_no_fieldname.mrv -67: -67: Test -67: -67: data_sgroup_empty_field_data.mrv -67: -67: Test -67: -67: radical_value.mrv -67: -67: Test -67: -67: emptyOneLineAtomList.mrv -67: -67: Test -67: -67: mrvValence_value.mrv -67: -67: Test -67: -67: ChiralTest2.mrv -67: -67: Test -67: -67: ChiralTest.mrv -67: -67: Test -67: -67: SnCl2.mrv -67: -67: Test -67: -67: SnH2Cl2.mrv -67: -67: Test -67: -67: marvin01.mrv -67: -67: Test -67: -67: marvin02.mrv -67: -67: Test -67: -67: marvin07.mrv -67: -67: Test -67: -67: marvin10.mrv -67: -67: Test -67: -67: marvin06.mrv -67: -67: Test -67: -67: marvin12.mrv -67: -67: Test -67: -67: EmptyMol.mrv -67: -67: Test -67: -67: Sparse.mrv -67: -67: Test -67: -67: Sparse2.mrv -67: -67: Test -67: -67: Sparse3.mrv -67: -67: Test -67: -67: MarvinNoCoords.mrv -67: -67: Test -67: -67: aspirin.mrv -67: -67: Test -67: -67: MarvinStereoGroupsZeros.mrv -67: -67: Test -67: -67: MarvinStereoGroupsAbs.mrv -67: -67: Test -67: -67: triphenylphosphine.mrv -67: -67: Test -67: -67: MarvinOldSuperGroupTest.mrv -67: -67: Test -67: -67: RadicalTests.mrv -67: -67: Test -67: -67: AnyBond.mrv -67: -67: Test -67: -67: cisBenzene.mrv -67: -67: Test -67: -67: DativeBond.mrv -67: -67: Test -67: -67: MultipleSgroup.mrv -67: -67: Test -67: -67: SgroupExpanded.mrv -67: -67: Test -67: -67: SgroupMultAttach.mrv -67: -67: Test -67: -67: MarvinMissingX2.mrv -67: -67: Test -67: -67: MarvinMissingY2.mrv -67: -67: Test -67: -67: DataSgroup.mrv -67: -67: Test -67: -67: MulticenterSgroup.mrv -67: -67: [06:21:44] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -94: [06:21:44] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [06:21:44] product atom-mapping number 2 not found in reactants. -67: [06:21:44] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -89: Randomness seeded to: 3783356868 -89: =============================================================================== -89: All tests passed (197 assertions in 9 test cases) -89: -94: [06:21:44] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [06:21:44] product atom-mapping number 2 not found in reactants. - 75/230 Test #89: substructTestCatch ..................... Passed 0.28 sec +87: [02:43:46] Explicit valence for atom # 3 Al, 6, is greater than permitted +68: [02:43:46] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [02:43:46] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 87/230 Test #96: pyChemReactionEnumerations .............***Exception: SegFault 0.43 sec + test 97 Start 97: pyChemReactionSanitize 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 97: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 -94: [06:21:44] CX Extensions: Substance group hierarchy is not always preserved. -94: [06:21:44] CX Extensions: Substance group hierarchy is not always preserved. -94: [06:21:44] reactant 0 has no mapped atoms. -94: [06:21:44] product 0 has no mapped atoms. -94: [06:21:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [06:21:44] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [06:21:44] Explicit valence for atom # 1 O, 5, is greater than permitted -94: =============================================================================== -94: All tests passed (702 assertions in 28 test cases) -94: - 76/230 Test #94: rxnTestCatch ........................... Passed 0.15 sec +68: [02:43:47] Empty atom list: 'M ALS 1 0 F' on line 8. + 88/230 Test #68: fileParsersTest1 ....................... Passed 9.07 sec test 98 Start 98: testChemTransforms 98: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 98: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 98: Test timeout computed to be: 1500 -59: Test -59: -59: Mrtx1719_3d.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop1.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop2.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop3.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop4.cxsmi -59: -59: Test -59: -59: Mrtx1719_atropBad1.cxsmi -59: -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -67: Test -67: -67: GenericSgroup.mrv -67: -67: Test -67: -67: MonomerSgroup.mrv -67: -67: Test -67: -67: modification_sgroup.mrv -67: -67: Test -67: -67: copolymer_sgroup.mrv -67: -67: Test -67: -67: MultipleSgroupParentInMiddleOfAtomBlock.mrv -67: -67: Test -67: -67: EmbeddedSgroups.mrv -67: -67: Test -67: -67: marvin03.mrv -67: -67: Test -67: -67: MarvinBadMissingMolID.mrv -67: -67: [06:21:44] -67: -67: **** -67: Test Assert -67: Expression Failed: -67: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -67: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -67: ---------- -67: Stacktrace: -67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 2# 0x565997A1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 3# 0x565A51D9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 4# 0x56590B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 5# 0xF7392D43 in /lib/i386-linux-gnu/libc.so.6 -67: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -67: 7# 0x56590C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: ---------- -67: **** -67: -67: Test -67: -67: MarvinBadMissingAtomID.mrv -67: -67: Expected id, elementType for an atom definition in MRV file -67: Test -67: -67: MarvinBadX2.mrv -67: -67: The values x2 and y2 must be large floats in MRV file -67: Test -67: -67: MarvinBadY2.mrv -67: -67: The values x2 and y2 must be large floats in MRV file -67: Test -67: -67: MarvinBadStereoGroupsAbs.mrv -67: -67: Unrecognized group definition 98: 1 smi: CC 98: 1 smi: CC 98: 2 smi: CCO[C@H](N)P -88: done 98: 2 smi: CC -67: Test -67: -67: MarvinBadElementType.mrv -67: -67: Test -67: -67: MarvinBadMissingBondID.mrv -67: -67: Test -67: -67: MarvinBadMissingBondAtomRefs -67: -67: Test -67: -67: MarvinBadMissingBondOrder.mrv -67: -67: bond must have one of: order, queryType, or convention in MRV File 98: replaceSub smi1:CCP(CC)[C@@H](N)O 98: replaceSub smi1:CCNCC -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test GitHub issue 15 -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test GitHub issue 409 98: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 98: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test chiral matching -67: Test -67: -67: MarvinBadMissingSruMolID.mrv -67: -67: Expected a molID in MRV file -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test dative-bond matching -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test cis/trans matching -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test cis/trans matching part 2 -67: Test -67: -67: MarvinBadMissingSruID.mrv -67: -67: Test -67: -67: MarvinBadMissingSruRole.mrv -67: -67: Test -67: -67: MarvinBadMissingSruAtomRef.mrv -67: -67: Test -67: -67: MarvinBadMissingSruTitle.mrv -67: -67: Test -67: -67: MarvinBadSruAtomRef.mrv -67: -67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -88: [06:21:44] done -88: [06:21:44] ------------------------------------- -88: [06:21:44] Testing matching E/Z against Cis/Trans stereo bonds -67: Test -67: -67: MarvinBadSruID.mrv -67: -67: Test -67: -67: MarvinBadSruRole.mrv -67: -67: Test -67: -67: MarvinBadSruAtomRef.mrv -67: -67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -67: Test -67: -67: MarvinBadSruAtomRef.mrv -67: -67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -88: [06:21:44] -88: -88: **** -88: Pre-condition Violation -88: matches must not be empty -88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -88: Failed Expression: !matches.empty() -88: ---------- -88: Stacktrace: -88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x56580B14 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x5657DEBA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0xF7454D43 in /lib/i386-linux-gnu/libc.so.6 -88: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -88: 8# 0x5657DFF7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: ---------- -88: **** -88: -88: [06:21:44] -88: -88: **** -88: Pre-condition Violation -88: matches must not be empty -88: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -88: Failed Expression: !matches.empty() -88: ---------- -88: Stacktrace: -88: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x56574D63 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x5657DEBA in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0xF7454D43 in /lib/i386-linux-gnu/libc.so.6 -88: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -88: 8# 0x5657DFF7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: ---------- -88: **** -88: -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test substructure matching with a pathological case for symmetric SSSR -88: [06:21:44] ------------------------------------- -88: [06:21:44] Test isAtomTerminalRGroupOrQueryHydrogen -67: Test -67: -67: MarvinBadSruConnect.mrv -67: -67: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -67: Test -67: -67: MarvinBadSupAttachAtom.mrv -67: -67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -67: Test -67: -67: MarvinBadSupAttachBond.mrv -67: -67: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -67: Test -67: -67: MarvinBadSupAttachOrder.mrv -67: -67: Order for an AttachmentPoint definition must be an integer in MRV file - 77/230 Test #88: testSubstructMatch ..................... Passed 0.39 sec +98: [02:43:47] SMARTS Parse Error: syntax error while parsing: bar +98: [02:43:47] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +87: [02:43:47] Explicit valence for atom # 4 Al, 6, is greater than permitted + 89/230 Test #98: testChemTransforms ..................... Passed 0.24 sec test 99 Start 99: chemTransformsTestCatch 99: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 99: Test timeout computed to be: 1500 -67: Test -67: -67: MarvinBadSupAttachAtom.mrv -67: -67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -67: Test -67: -67: MarvinBadSupAttachAtom.mrv -67: -67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -67: Test -67: -67: MarvinBadSupAttachAtom.mrv -67: -67: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -67: Test -67: -67: MarvinBadSupMissingAttachBond.mrv -67: -67: No attachment point found for bond to the condensed atom in a superatomSgroup -93: 30000000 30000000 -98: [06:21:44] SMARTS Parse Error: syntax error while parsing: bar -98: [06:21:44] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -67: Test -67: -67: MarvinBadSupMissingAttachOrder.mrv -67: -67: Expected atom, order and bond, for an AttachmentPoint definition in MRV file - 78/230 Test #98: testChemTransforms ..................... Passed 0.10 sec + 90/230 Test #97: pyChemReactionSanitize .................***Exception: SegFault 0.39 sec + test 100 Start 100: tautomerQueryTestCatch 100: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery 100: Test timeout computed to be: 1500 -99: Randomness seeded to: 357599578 -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] +87: [02:43:47] Explicit valence for atom # 10 Si, 6, is greater than permitted +99: Randomness seeded to: 756720215 +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23041,21 +25328,21 @@ 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x565D2638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 4# 0x56657638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 13# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 13# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23068,21 +25355,21 @@ 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x565D2638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 4# 0x56657638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 13# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 13# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23095,23 +25382,23 @@ 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x565D2638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 4# 0x56657638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 13# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 13# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23124,95 +25411,21 @@ 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x565D2638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 4# 0x56657638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 13# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 13# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: - 79/230 Test #95: pyChemReactions ........................***Exception: SegFault 0.31 sec - -test 101 - Start 101: pyTautomerQuery - -101: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -101: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -101: Test timeout computed to be: 1500 -67: Test -67: -67: marvin03.mrv -67: -67: Test -67: -67: Cubane.mrv -67: -67: Test -67: -67: FalseAtropisomer.mrv -67: -67: Test -67: -67: AtropEnhancedStereo.mrv -67: -67: Test -67: -67: AtropManyChirals.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced2.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced3.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced4.mrv -67: -67: Test -67: -67: BMS-986142_3d_chiral.mrv -67: -67: Test -67: -67: BMS-986142_3d.mrv -67: -67: Test -67: -67: BMS-986142_atrop1.mrv -67: -67: Test -67: -67: BMS-986142_atrop2.mrv -67: -67: Test -67: -67: BMS-986142_atrop3.mrv -67: -67: Test -67: -67: BMS-986142_atrop4.mrv -67: -67: Test -67: -67: BMS-986142_atrop5.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -99: [06:21:44] Incomplete atom labelling, cannot make bond -99: [06:21:44] +99: [02:43:47] Incomplete atom labelling, cannot make bond +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23225,20 +25438,20 @@ 99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x565D2638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 4# 0x56657638 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 13# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 13# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: -99: [06:21:44] +99: [02:43:47] 99: 99: **** 99: Invariant Violation @@ -23252,54 +25465,61 @@ 99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 5# 0x565C74A2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x566277BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x5662849F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x56628B04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x565F7BA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x565F7F32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x565C6776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 12# 0xF736AD43 in /lib/i386-linux-gnu/libc.so.6 +99: 5# 0x5664C4A2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x566AC7BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x566AD49F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x566ADB04 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x5667CBA4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x5667CF32 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x5664B776 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 12# 0xF7306D43 in /lib/i386-linux-gnu/libc.so.6 99: 13# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -99: 14# 0x565C67B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 14# 0x5664B7B7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 99: ---------- 99: **** 99: 99: =============================================================================== 99: All tests passed (674 assertions in 9 test cases) 99: - 80/230 Test #99: chemTransformsTestCatch ................ Passed 0.15 sec + 91/230 Test #99: chemTransformsTestCatch ................ Passed 0.36 sec +test 101 + Start 101: pyTautomerQuery + +101: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +101: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +101: Test timeout computed to be: 1500 +100: Randomness seeded to: 3598185145 +100: =============================================================================== +100: All tests passed (93 assertions in 13 test cases) +100: + 92/230 Test #100: tautomerQueryTestCatch ................. Passed 0.45 sec test 102 Start 102: testSubgraphs1 102: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 102: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 102: Test timeout computed to be: 1500 -67: Test -67: -67: BMS-986142_atrop6.mrv -67: -67: Test -67: -67: BMS-986142_atrop7.mrv -67: -67: Test -67: -67: BMS-986142_atrop8.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 102: ----------------------- 102: Subgraph retrieval 102: Finished 102: ----------------------- 102: testSubgraphs2a -67: Test -67: -67: BMS-986142_atropBad2.mrv -67: -67: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 - 81/230 Test #96: pyChemReactionEnumerations .............***Exception: SegFault 0.33 sec +102: Finished +102: ----------------------- +102: testSubgraphs2 +102: Finished +102: ----------------------- +102: Path retrieval +102: Finished +102: ----------------------- +102: Path retrieval2 +102: Finished +102: ----------------------- +102: Unique Subgraph retrieval +102: Finished +102: ----------------------- +102: testUniqueSubgraphs2 + 93/230 Test #101: pyTautomerQuery ........................***Exception: SegFault 0.64 sec test 103 Start 103: testSubgraphs2 @@ -23307,40 +25527,8 @@ 103: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 103: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 103: Test timeout computed to be: 1500 -102: Finished -102: ----------------------- -102: testSubgraphs2 103: ----------------------- 103: Test1: pathToSubmol - 82/230 Test #97: pyChemReactionSanitize .................***Exception: SegFault 0.28 sec - -test 104 - Start 104: subgraphsCatch - -104: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 -67: Test -67: -67: JDQ443_3d.mrv -67: -67: Test -67: -67: JDQ443_atrop1.mrv -67: -67: Test -67: -67: JDQ443_atrop2.mrv -67: -67: Test -67: -67: JDQ443_atrop3.mrv -67: -67: Test -67: -67: JDQ443_atropBad1.mrv -67: -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 103: Finished 103: ----------------------- 103: Test2: Atom Environments @@ -23354,116 +25542,28 @@ 103: ----------------------- 103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 103: Finished -67: Test -67: -67: RP-6306_atrop1.mrv -67: -67: Test -67: -67: RP-6306_atrop2.mrv -67: -67: Test -67: -67: RP-6306_atrop3.mrv -67: -67: Test -67: -67: RP-6306_atrop4.mrv -67: -67: Test -67: -67: RP-6306_atrop5.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored - 83/230 Test #103: testSubgraphs2 ......................... Passed 0.06 sec -test 105 - Start 105: filterCatalogTest + 94/230 Test #103: testSubgraphs2 ......................... Passed 0.06 sec +test 104 + Start 104: subgraphsCatch -105: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog -105: Test timeout computed to be: 1500 -67: Test -67: -67: RP-6306_atropBad1.mrv -67: -67: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -67: Test -67: -67: RP-6306_atropBad2.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -104: Randomness seeded to: 707118794 +104: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +104: Randomness seeded to: 3317408888 104: --------- 104: =============================================================================== 104: All tests passed (11 assertions in 1 test case) 104: - 84/230 Test #104: subgraphsCatch ......................... Passed 0.05 sec -test 106 - Start 106: pyFilterCatalog + 95/230 Test #104: subgraphsCatch ......................... Passed 0.06 sec +test 105 + Start 105: filterCatalogTest -106: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -106: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -106: Test timeout computed to be: 1500 -87: Randomness seeded to: 3688883626 -87: [06:21:44] Explicit valence for atom # 9 N, 6, is greater than permitted -102: Finished -102: ----------------------- -102: Path retrieval -102: Finished -102: ----------------------- -102: Path retrieval2 -102: Finished -102: ----------------------- -102: Unique Subgraph retrieval -102: Finished -102: ----------------------- -102: testUniqueSubgraphs2 -67: Test -67: -67: RP-6306_3d.mrv -67: -67: Test -67: -67: Sotorasib_atrop1.mrv -67: -67: Test -67: -67: Sotorasib_atrop2.mrv -67: -67: Test -67: -67: Sotorasib_atrop3.mrv -67: -67: Test -67: -67: Sotorasib_atrop4.mrv -67: -67: Test -67: -67: Sotorasib_atrop5.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -34: [06:21:44] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. -67: Test -67: -67: Sotorasib_atropBad1.mrv -67: -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -67: Test -67: -67: Sotorasib_atropBad2.mrv -67: -67: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -34: F/C=C/Cl -34: [H]/C(F)=C(/[H])Cl -34: F/C=C/Cl -34: F/C=C/Cl -34: C/C(F)=C(/C)Cl +105: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog +105: Test timeout computed to be: 1500 +87: [02:43:48] Explicit valence for atom # 2 O, 4, is greater than permitted +87: [02:43:48] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [02:43:48] Explicit valence for atom # 3 Be, 4, is greater than permitted 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason hzone_phenol_A(479) 105: v = { @@ -23490,10 +25590,6 @@ 105: 8,16}, 105: 9,21}, 105: } -100: Randomness seeded to: 1067330546 -100: =============================================================================== -100: All tests passed (93 assertions in 13 test cases) -100: 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason cyano_imine_B(17) 105: v = { @@ -23526,2663 +25622,122 @@ 105: 11,17}, 105: 12,16}, 105: } - 85/230 Test #100: tautomerQueryTestCatch ................. Passed 0.28 sec -test 107 - Start 107: testFragCatalog - -107: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog -107: Test timeout computed to be: 1500 -34: [06:21:44] ----------------------- -34: Testing isRingFused 105: Warning: molecule failed filter -105: Warning: molecule failed filter: reason keto_keto_gamma(5) -105: v = { -105: 0,0}, -105: 1,1}, -105: 2,2}, -105: 3,4}, -105: 4,5}, -105: 5,6}, -105: 6,7}, -105: 7,8}, -105: 8,9}, -105: 9,14}, -105: 10,15}, -105: 11,16}, -105: } -105: match = { -105: 0,0}, -105: 1,1}, -105: 2,2}, -105: 3,4}, -105: 4,5}, -105: 5,6}, -105: 6,7}, -105: 7,8}, -105: 8,9}, -105: 9,14}, -105: 10,15}, -105: 11,16}, -105: } - 86/230 Test #34: graphmolMolOpsTest ..................... Passed 1.36 sec -test 108 - Start 108: pyFragCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap -108: Test timeout computed to be: 1500 -67: Test -67: -67: Sotorasib_3d.mrv -67: -67: Test -67: -67: ZM374979_atrop1.mrv -67: -67: Test -67: -67: ZM374979_atrop2.mrv -67: -67: Test -67: -67: ZM374979_atrop3.mrv -67: -67: Test -67: -67: ZM374979_atropBad1.mrv -67: -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 87/230 Test #101: pyTautomerQuery ........................***Exception: SegFault 0.26 sec - -test 109 - Start 109: testDescriptors - -109: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -109: Test timeout computed to be: 1500 -90: Randomness seeded to: 2046550535 -90: =============================================================================== -90: All tests passed (11480 assertions in 38 test cases) -90: -107: 21 -67: Test -67: -67: mrtx1719_3d.mrv -67: -67: Test -67: -67: mrtx1719_atrop1.mrv -67: -67: Test -67: -67: mrtx1719_atrop2.mrv -67: -67: Test -67: -67: mrtx1719_atrop3.mrv -67: -67: Test -67: -67: mrtx1719_atropBad1.mrv -67: -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -68: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored - 88/230 Test #90: testGenericGroups ...................... Passed 0.71 sec -test 110 - Start 110: testAUTOCORR2D - -110: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -110: Test timeout computed to be: 1500 -68: [06:21:44] deprecated group abbreviation ignored on line 24 -68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -68: [06:21:44] -68: -68: **** -68: Post-condition Violation -68: Element 'Mv' not found -68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -68: Failed Expression: anum > -1 -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0xF7DADCC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0xF7DB75D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 7# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 8# 0x565B7F80 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 9# 0x5662AE79 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x5659CC18 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0xF746CD43 in /lib/i386-linux-gnu/libc.so.6 -68: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -68: 13# 0x5659CDB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -110: [06:21:44] ---------------------------- -110: start test autocorr2D -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Crippen parameter acquisition. -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Crippen calculation. -87: [06:21:44] Explicit valence for atom # 3 Al, 6, is greater than permitted -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Issue262: problems with Crippen calculation from pickles. -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test AMW calculation. -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Exact MW calculation. -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Labute ASA descriptors. -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test TPSA descriptors. -3: dynamic RDAny:0.611208 s -3: static RDValue:1e-06 s -67: Test -67: -67: FalseAtropisomer.mrv -67: -67: Test -67: -67: AtropEnhancedStereo.mrv -67: -67: Test -67: -67: AtropManyChirals.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced2.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced3.mrv -67: -67: Test -67: -67: AtropManyChiralsEnhanced4.mrv -67: -67: Test -67: -67: BMS-986142_3d_chiral.mrv -67: -67: Test -67: -67: BMS-986142_3d.mrv -67: -67: Test -67: -67: BMS-986142_atrop1.mrv -67: -67: Test -67: -67: BMS-986142_atrop2.mrv -67: -67: Test -67: -67: BMS-986142_atrop3.mrv -67: -67: Test -67: -67: BMS-986142_atrop4.mrv -67: -67: Test -67: -67: BMS-986142_atrop5.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -87: [06:21:44] Explicit valence for atom # 4 Al, 6, is greater than permitted -67: Test -67: -67: BMS-986142_atrop6.mrv -67: -67: Test -67: -67: BMS-986142_atrop7.mrv -67: -67: Test -67: -67: BMS-986142_atrop8.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -109: [06:21:44] done -109: [06:21:44] ------------------------------------- -109: [06:21:44] Test Lipinski parameters. -67: Test -67: -67: BMS-986142_atropBad2.mrv -67: -67: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 - 89/230 Test #106: pyFilterCatalog ........................***Exception: SegFault 0.28 sec - -test 111 - Start 111: testATF - -111: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF -111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 - 90/230 Test #105: filterCatalogTest ...................... Passed 0.30 sec -test 112 - Start 112: testBCUT - -112: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT -112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -112: Test timeout computed to be: 1500 -102: Finished -102: ----------------------- -102: testRootedSubgraphs -102: Finished -102: ----------------------- -102: testRootedPaths -102: Finished -3: dynamic RDValue:0.069138 s -3: deleted! -3: [06:21:44] ------------------------------------- -3: [06:21:44] Testing String Pickle Roundtrips. -3: [06:21:44] done -3: [06:21:44] ------------------------------------- -3: [06:21:44] Testing conversion of vect to string. -3: [06:21:44] done -3: [06:21:44] ------------------------------------- -3: [06:21:44] Testing returning const references. -3: [06:21:44] any cast - 91/230 Test #102: testSubgraphs1 ......................... Passed 0.39 sec -test 113 - Start 113: testEEM - -113: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM -113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -3: [06:21:44] done: 0.002025 300000 -3: [06:21:44] copy -3: [06:21:44] done: 0.002037 300000 -3: [06:21:44] ref -3: [06:21:44] done: 0.00202 300000 -3: [06:21:44] dict -3: [06:21:44] done: 0.004021 300000 -3: [06:21:44] ref with hasVal -3: [06:21:44] done: 0.00289 300000 -3: [06:21:44] done -3: [06:21:44] ------------------------------------- -3: [06:21:44] Testing dict update. -3: [06:21:44] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -112: [06:21:44] ------------------------------------- -112: [06:21:44] Basic BCUT tests. -87: [06:21:44] Explicit valence for atom # 10 Si, 6, is greater than permitted - 92/230 Test #3: testDict ............................... Passed 1.65 sec - 93/230 Test #111: testATF ................................ Passed 0.04 sec -test 114 - Start 114: testPBF - -114: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF -114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -test 115 - Start 115: testRDFcustom - -115: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -112: [06:21:44] done -112: [06:21:44] ------------------------------------- -112: [06:21:44] Larger BCUT tests. -67: Test -67: -67: JDQ443_3d.mrv -67: -67: Test -67: -67: JDQ443_atrop1.mrv -67: -67: Test -67: -67: JDQ443_atrop2.mrv -67: -67: Test -67: -67: JDQ443_atrop3.mrv -67: -67: Test -67: -67: JDQ443_atropBad1.mrv -67: -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -67: Test -67: -67: RP-6306_atrop1.mrv -67: -67: Test -67: -67: RP-6306_atrop2.mrv -67: -67: Test -67: -67: RP-6306_atrop3.mrv -67: -67: Test -67: -67: RP-6306_atrop4.mrv -67: -67: Test -67: -67: RP-6306_atrop5.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -113: =>start test EEM -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 0 -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:44] 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: [06:21:44] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -67: Test -67: -67: RP-6306_atropBad1.mrv -67: -67: [06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -114: [06:21:44] ------------------------------------- -114: [06:21:44] Basic PBF tests. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: RP-6306_atropBad2.mrv -67: -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: RP-6306_3d.mrv -67: -67: Test -67: -67: Sotorasib_atrop1.mrv -67: -67: Test -67: -67: Sotorasib_atrop2.mrv -67: -67: Test -67: -67: Sotorasib_atrop3.mrv -67: -67: Test -67: -67: Sotorasib_atrop4.mrv -67: -67: Test -67: -67: Sotorasib_atrop5.mrv -67: -67: [06:21:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [06:21:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: Sotorasib_atropBad1.mrv -67: -67: [06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: Sotorasib_atropBad2.mrv -67: -67: [06:21:45] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 94/230 Test #108: pyFragCatalog ..........................***Exception: SegFault 0.32 sec - -test 116 - Start 116: testRDF - -116: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF -116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: ---------------------------------- -68: ---------------------------------- -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: [06:21:45] done -109: [06:21:45] ------------------------------------- -109: [06:21:45] Test VSA descriptors. -109: [06:21:45] done -109: [06:21:45] ------------------------------------- -109: [06:21:45] Test molecular formula calculation. -109: [06:21:45] done -109: [06:21:45] ------------------------------------- -109: [06:21:45] Test Issue 3415534. -109: [06:21:45] done -109: [06:21:45] ------------------------------------- -109: [06:21:45] Test Issue3433771: Bad definition for Crippen atom type O11. -68: [06:21:45] -68: -68: **** -68: Pre-condition Violation -68: rlabel out of range for MDL files -68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -68: Failed Expression: rlabel >= 0 && rlabel < 100 -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x565C7582 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x5662AEF1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x5659CC18 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0xF746CD43 in /lib/i386-linux-gnu/libc.so.6 -68: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -68: 8# 0x5659CDB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -68: [06:21:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -109: [06:21:45] done -109: [06:21:45] ------------------------------------- -109: [06:21:45] Test multithreading -109: reading molecules -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: Sotorasib_3d.mrv -67: -67: Test -67: -67: ZM374979_atrop1.mrv -67: -67: Test -67: -67: ZM374979_atrop2.mrv -67: -67: Test -67: -67: ZM374979_atrop3.mrv -67: -67: Test -67: -67: ZM374979_atropBad1.mrv -67: -67: [06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 100 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: processing -109: launch :0 -109: launch :1 -109: launch :2 -109: launch :3 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: mrtx1719_3d.mrv -67: -67: Test -67: -67: mrtx1719_atrop1.mrv -67: -67: Test -67: -67: mrtx1719_atrop2.mrv -67: -67: Test -67: -67: mrtx1719_atrop3.mrv -67: -67: Test -67: -67: mrtx1719_atropBad1.mrv -67: -67: [06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: [06:21:45] Explicit valence for atom # 2 O, 4, is greater than permitted -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: [06:21:45] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [06:21:45] Explicit valence for atom # 3 Be, 4, is greater than permitted -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [06:21:45] done -114: [06:21:45] ------------------------------------- -114: [06:21:45] PBF edge cases. -114: [06:21:45] done - 95/230 Test #114: testPBF ................................ Passed 0.29 sec -test 117 - Start 117: testMORSE - -117: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE -117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: [06:21:45] Explicit valence for atom # 27 P, 6, is greater than permitted -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 200 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: AlexRxn.mrv -67: -67: Test -67: -67: BadReactionSign.mrv -67: -67: Test -67: -67: bondArray_node.mrv -67: -67: Test -67: -67: marvin03.mrv -67: -67: Test -67: -67: marvin04.mrv -67: -67: Test -67: -67: marvin08.mrv -67: -67: Test -67: -67: marvin09.mrv -67: -67: Test -67: -67: marvin11.mrv -67: -67: Test -67: -67: marvin05.mrv -67: -67: Test -67: -67: EmptyRxn.mrv -67: -67: [06:21:45] initialization failed -110: [06:21:45] done -110: [06:21:45] ------------------------------------- -110: [06:21:45] Test Github #3806: NaNs from AUTOCORR2D descriptor -110: [06:21:45] done -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 96/230 Test #110: testAUTOCORR2D ......................... Passed 0.51 sec -test 118 - Start 118: test3D - -118: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D -118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: Test -67: -67: RxnNoCoords.mrv -67: -67: Test -67: -67: mrvValenceZero.mrv -67: -67: Test -67: -67: condition_coordinates_mpoint.mrv -67: -67: Test -67: -67: marvin01.mrv -67: -67: Test -67: -67: aspirineSynthesisWithAttributes.mrv -67: -67: Test -67: -67: marvin01.mrv -67: -67: Test -67: -67: NewChiralTest -67: -67: [06:21:45] -67: -67: **** -67: Test Assert -67: Expression Failed: -67: Violation occurred on line 237 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -67: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -67: ---------- -67: Stacktrace: -67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 2# 0x565949B9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 3# 0x565AAB0B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 4# 0x56590B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 5# 0xF7392D43 in /lib/i386-linux-gnu/libc.so.6 -67: 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -67: 7# 0x56590C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: ---------- -67: **** -67: -67: terminate called after throwing an instance of 'Invar::Invariant' -67: what(): Expression Failed: - 97/230 Test #67: testMrvToMol ...........................Subprocess aborted***Exception: 1.64 sec -Using new chirality perception -Test - - rxnStereoMarkedCrossed.mrv - -Test - - NewChiralTest.sdf - -Test - - NewChiralTest.sdf - -Test - - NewChiralTestNoChiral.sdf - -Test - - NewChiralTestNoChiral.sdf - -Test - - NewChiralTestAllChiral.sdf - -Test - - NewChiralTestAllChiral.sdf - -Test - - vendor839.sdf - -Test - - ProblemShort.mol - -[06:21:43] For a MultipleSgroup expansion, the matching orphaned bond was not found -The multiple sgroup will be ignored -Test - - badWedgeError.sdf - -Test - - CrossedDoubleBondWithChiralNbr2.sdf - -Test - - CrossedDoubleBondWithChiralNbr.sdf - -Test - - SimpleWiggleDoubleBond.sdf - -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 - - BadRxn.rxn - -Test - - FalseChiral.mrv - -Test - - FalseChiral.mrv - -Test - - Cubane.mrv - -Test - - NewChiralTest.mrv - -Test - - NewChiralTest.mrv - -Test - - NewChiralTestNoChiral.mrv - -Test - - NewChiralTestNoChiral.mrv - -Test - - NewChiralTestAllChiral.mrv - -Test - - NewChiralTestAllChiral.mrv - -Test - - DataSgroupMissingUnitsDisplayed.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 - -[06:21:44] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -[06:21:44] 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 - -[06:21:44] - -**** -Test Assert -Expression Failed: -Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr ----------- -Stacktrace: - 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 2# 0x565997A1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 3# 0x565A51D9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 4# 0x56590B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 5# 0xF7392D43 in /lib/i386-linux-gnu/libc.so.6 - 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 - 7# 0x56590C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol ----------- -**** - -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 - - Cubane.mrv - -Test - - FalseAtropisomer.mrv - -Test - - AtropEnhancedStereo.mrv - -Test - - AtropManyChirals.mrv - -Test - - AtropManyChiralsEnhanced.mrv - -Test - - AtropManyChiralsEnhanced2.mrv - -Test - - AtropManyChiralsEnhanced3.mrv - -Test - - AtropManyChiralsEnhanced4.mrv - -Test - - BMS-986142_3d_chiral.mrv - -Test - - BMS-986142_3d.mrv - -Test - - BMS-986142_atrop1.mrv - -Test - - BMS-986142_atrop2.mrv - -Test - - BMS-986142_atrop3.mrv - -Test - - BMS-986142_atrop4.mrv - -Test - - BMS-986142_atrop5.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - BMS-986142_atrop6.mrv - -Test - - BMS-986142_atrop7.mrv - -Test - - BMS-986142_atrop8.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - BMS-986142_atropBad2.mrv - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -Test - - JDQ443_3d.mrv - -Test - - JDQ443_atrop1.mrv - -Test - - JDQ443_atrop2.mrv - -Test - - JDQ443_atrop3.mrv - -Test - - JDQ443_atropBad1.mrv - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -Test - - RP-6306_atrop1.mrv - -Test - - RP-6306_atrop2.mrv - -Test - - RP-6306_atrop3.mrv - -Test - - RP-6306_atrop4.mrv - -Test - - RP-6306_atrop5.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -Test - - RP-6306_atropBad1.mrv - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -Test - - RP-6306_atropBad2.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -Test - - RP-6306_3d.mrv - -Test - - Sotorasib_atrop1.mrv - -Test - - Sotorasib_atrop2.mrv - -Test - - Sotorasib_atrop3.mrv - -Test - - Sotorasib_atrop4.mrv - -Test - - Sotorasib_atrop5.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - Sotorasib_atropBad1.mrv - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -Test - - Sotorasib_atropBad2.mrv - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -Test - - Sotorasib_3d.mrv - -Test - - ZM374979_atrop1.mrv - -Test - - ZM374979_atrop2.mrv - -Test - - ZM374979_atrop3.mrv - -Test - - ZM374979_atropBad1.mrv - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -Test - - mrtx1719_3d.mrv - -Test - - mrtx1719_atrop1.mrv - -Test - - mrtx1719_atrop2.mrv - -Test - - mrtx1719_atrop3.mrv - -Test - - mrtx1719_atropBad1.mrv - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -Test - - FalseAtropisomer.mrv - -Test - - AtropEnhancedStereo.mrv - -Test - - AtropManyChirals.mrv - -Test - - AtropManyChiralsEnhanced.mrv - -Test - - AtropManyChiralsEnhanced2.mrv - -Test - - AtropManyChiralsEnhanced3.mrv - -Test - - AtropManyChiralsEnhanced4.mrv - -Test - - BMS-986142_3d_chiral.mrv - -Test - - BMS-986142_3d.mrv - -Test - - BMS-986142_atrop1.mrv - -Test - - BMS-986142_atrop2.mrv - -Test - - BMS-986142_atrop3.mrv - -Test - - BMS-986142_atrop4.mrv - -Test - - BMS-986142_atrop5.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - BMS-986142_atrop6.mrv - -Test - - BMS-986142_atrop7.mrv - -Test - - BMS-986142_atrop8.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - BMS-986142_atropBad2.mrv - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -Test - - JDQ443_3d.mrv - -Test - - JDQ443_atrop1.mrv - -Test - - JDQ443_atrop2.mrv - -Test - - JDQ443_atrop3.mrv - -Test - - JDQ443_atropBad1.mrv - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -Test - - RP-6306_atrop1.mrv - -Test - - RP-6306_atrop2.mrv - -Test - - RP-6306_atrop3.mrv - -Test - - RP-6306_atrop4.mrv - -Test - - RP-6306_atrop5.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -Test - - RP-6306_atropBad1.mrv - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -Test - - RP-6306_atropBad2.mrv - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -Test - - RP-6306_3d.mrv - -Test - - Sotorasib_atrop1.mrv - -Test - - Sotorasib_atrop2.mrv - -Test - - Sotorasib_atrop3.mrv - -Test - - Sotorasib_atrop4.mrv - -Test - - Sotorasib_atrop5.mrv - -[06:21:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - Sotorasib_atropBad1.mrv - -[06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -Test - - Sotorasib_atropBad2.mrv - -[06:21:45] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -Test - - Sotorasib_3d.mrv - -Test - - ZM374979_atrop1.mrv - -Test - - ZM374979_atrop2.mrv - -Test - - ZM374979_atrop3.mrv - -Test - - ZM374979_atropBad1.mrv - -[06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -Test - - mrtx1719_3d.mrv - -Test - - mrtx1719_atrop1.mrv - -Test - - mrtx1719_atrop2.mrv - -Test - - mrtx1719_atrop3.mrv - -Test - - mrtx1719_atropBad1.mrv - -[06:21:45] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -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 - -[06:21:45] initialization failed -Test - - RxnNoCoords.mrv - -Test - - mrvValenceZero.mrv - -Test - - condition_coordinates_mpoint.mrv - -Test - - marvin01.mrv - -Test - - aspirineSynthesisWithAttributes.mrv - -Test - - marvin01.mrv - -Test - - NewChiralTest - -[06:21:45] - -**** -Test Assert -Expression Failed: -Violation occurred on line 237 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr ----------- -Stacktrace: - 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 2# 0x565949B9 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 3# 0x565AAB0B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 4# 0x56590B0C in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol - 5# 0xF7392D43 in /lib/i386-linux-gnu/libc.so.6 - 6# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 - 7# 0x56590C97 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol ----------- -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - -test 119 - Start 119: testWHIM - -119: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testWHIM -119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: [06:21:45] ------------------------------------- -118: [06:21:45] Basic PMI tests. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 300 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: Test -59: -59: AtropCanon1.cxsmi -59: -59: Test -59: -59: AtropCanon2.cxsmi -59: -59: Test -59: -59: AtropCanon3.cxsmi -59: -59: Test -59: -59: BMS-986142_3d_chiral.cxsmi -59: -59: Test -59: -59: BMS-986142_3d.cxsmi -59: -59: =============================================================================== -59: test cases: 29 | 28 passed | 1 failed -59: assertions: 2445 | 2444 passed | 1 failed -59: -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 98/230 Test #59: cxsmilesTest ...........................***Failed 1.81 sec -Randomness seeded to: 3468599647 -Test - - ShortAtropisomerNoCoords.cxsmi - - -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cxsmilesTest is a Catch2 v3.7.1 host application. -Run with -? for options - -------------------------------------------------------------------------------- -testAtropisomersInCXSmiles -------------------------------------------------------------------------------- -./Code/GraphMol/SmilesParse/cxsmiles_test.cpp:1030 -............................................................................... - -./Code/GraphMol/SmilesParse/cxsmiles_test.cpp:818: FAILED: - CHECK( getExpectedValue(expectedFileName) == outMolStr ) -with expansion: - " - RDKit 2D - - 0 0 0 0 0 0 0 0 0 0999 V3000 - M V30 BEGIN CTAB - M V30 COUNTS 14 15 0 0 0 - M V30 BEGIN ATOM - M V30 1 C 3.000000 0.000000 0.000000 0 - M V30 2 C 1.500000 0.000000 0.000000 0 - M V30 3 C 0.750000 -1.299038 0.000000 0 - M V30 4 N 1.500000 -2.598076 0.000000 0 - M V30 5 C 2.991783 -2.754869 0.000000 0 - M V30 6 C 3.303650 -4.222090 0.000000 0 - M V30 7 C 2.004612 -4.972090 0.000000 0 - M V30 8 C 0.889895 -3.968394 0.000000 0 - M V30 9 C -0.577326 -4.280262 0.000000 0 - M V30 10 C -0.750000 -1.299038 0.000000 0 - M V30 11 C -1.500000 -2.598076 0.000000 0 - M V30 12 C -1.500000 0.000000 0.000000 0 - M V30 13 C -0.750000 1.299038 0.000000 0 - M V30 14 C 0.750000 1.299038 0.000000 0 - M V30 END ATOM - M V30 BEGIN BOND - M V30 1 1 1 2 - M V30 2 2 2 3 - M V30 3 1 3 4 - M V30 4 1 4 5 - M V30 5 2 5 6 - M V30 6 1 6 7 - M V30 7 2 7 8 - M V30 8 1 8 9 - M V30 9 1 3 10 CFG=1 - M V30 10 1 10 11 - M V30 11 1 10 12 - M V30 12 1 12 13 - M V30 13 1 13 14 - M V30 14 1 14 2 - M V30 15 1 8 4 - M V30 END BOND - M V30 END CTAB - M END - " - == - " - RDKit 2D - - 0 0 0 0 0 0 0 0 0 0999 V3000 - M V30 BEGIN CTAB - M V30 COUNTS 14 15 0 0 0 - M V30 BEGIN ATOM - M V30 1 C 3.000000 -0.000000 0.000000 0 - M V30 2 C 1.500000 0.000000 0.000000 0 - M V30 3 C 0.750000 -1.299038 0.000000 0 - M V30 4 N 1.500000 -2.598076 0.000000 0 - M V30 5 C 2.991783 -2.754869 0.000000 0 - M V30 6 C 3.303650 -4.222090 0.000000 0 - M V30 7 C 2.004612 -4.972090 0.000000 0 - M V30 8 C 0.889895 -3.968394 0.000000 0 - M V30 9 C -0.577326 -4.280262 0.000000 0 - M V30 10 C -0.750000 -1.299038 0.000000 0 - M V30 11 C -1.500000 -2.598076 0.000000 0 - M V30 12 C -1.500000 0.000000 0.000000 0 - M V30 13 C -0.750000 1.299038 0.000000 0 - M V30 14 C 0.750000 1.299038 0.000000 0 - M V30 END ATOM - M V30 BEGIN BOND - M V30 1 1 1 2 - M V30 2 2 2 3 - M V30 3 1 3 4 - M V30 4 1 4 5 - M V30 5 2 5 6 - M V30 6 1 6 7 - M V30 7 2 7 8 - M V30 8 1 8 9 - M V30 9 1 3 10 CFG=1 - M V30 10 1 10 11 - M V30 11 1 10 12 - M V30 12 1 12 13 - M V30 13 1 13 14 - M V30 14 1 14 2 - M V30 15 1 8 4 - M V30 END BOND - M V30 END CTAB - M END - " -with message: - /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/test_data/ - ShortAtropisomerNoCoords.cxsmi - -Test - - ShortAtropisomer.cxsmi - -Test - - ShortAtropisomerArom.cxsmi - -Test - - AtropManyChirals.cxsmi - -Test - - AtropManyChiralsEnhanced.cxsmi - -Test - - AtropManyChiralsEnhanced2.cxsmi - -Test - - AtropManyChiralsEnhanced3.cxsmi - -Test - - AtropManyChiralsEnhanced4.cxsmi - -Test - - BMS-986142_3d_chiral.cxsmi - -Test - - BMS-986142_3d.cxsmi - -Test - - BMS-986142_atrop1.cxsmi - -Test - - BMS-986142_atrop2.cxsmi - -Test - - BMS-986142_atrop3.cxsmi - -Test - - BMS-986142_atrop4.cxsmi - -Test - - BMS-986142_atrop5.cxsmi - -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:43] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - BMS-986142_atrop6.cxsmi - -Test - - BMS-986142_atropBad1.cxsmi - -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -Test - - BMS-986142_atropBad2.cxsmi - -[06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -[06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -[06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -[06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -[06:21:43] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -Test - - JDQ443_3d.cxsmi - -Test - - JDQ443_atrop1.cxsmi - -Test - - JDQ443_atrop2.cxsmi - -Test - - JDQ443_atrop3.cxsmi - -Test - - JDQ443_atrop4.cxsmi - -Test - - JDQ443_atropBad1.cxsmi - -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -[06:21:43] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -Test - - RP-6306_atrop1.cxsmi - -Test - - RP-6306_atrop2.cxsmi - -Test - - RP-6306_atrop3.cxsmi - -Test - - RP-6306_atrop4.cxsmi - -Test - - RP-6306_atrop5.cxsmi - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -Test - - RP-6306_atrop6.cxsmi - -Test - - RP-6306_atropBad1.cxsmi - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -Test - - RP-6306_atropBad2.cxsmi - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -Test - - RP-6306_3d.cxsmi - -Test - - Sotorasib_atrop1.cxsmi - -Test - - Sotorasib_atrop2.cxsmi - -Test - - Sotorasib_atrop3.cxsmi - -Test - - Sotorasib_atrop4.cxsmi - -Test - - Sotorasib_atrop5.cxsmi - -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -[06:21:44] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -Test - - Sotorasib_atropBad1.cxsmi - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -Test - - Sotorasib_atropBad2.cxsmi - -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -[06:21:44] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -Test - - Sotorasib_3d.cxsmi - -Test - - ZM374979_atrop1.cxsmi - -Test - - ZM374979_atrop2.cxsmi - -Test - - ZM374979_atrop3.cxsmi - -Test - - ZM374979_atrop4.cxsmi - -Test - - ZM374979_atropBad1.cxsmi - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -Test - - Mrtx1719_3d.cxsmi - -Test - - Mrtx1719_atrop1.cxsmi - -Test - - Mrtx1719_atrop2.cxsmi - -Test - - Mrtx1719_atrop3.cxsmi - -Test - - Mrtx1719_atrop4.cxsmi - -Test - - Mrtx1719_atropBad1.cxsmi - -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -[06:21:44] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -Test - - AtropCanon1.cxsmi - -Test - - AtropCanon2.cxsmi - -Test - - AtropCanon3.cxsmi - -Test - - BMS-986142_3d_chiral.cxsmi - -Test +105: Warning: molecule failed filter: reason keto_keto_gamma(5) +105: v = { +105: 0,0}, +105: 1,1}, +105: 2,2}, +105: 3,4}, +105: 4,5}, +105: 5,6}, +105: 6,7}, +105: 7,8}, +105: 8,9}, +105: 9,14}, +105: 10,15}, +105: 11,16}, +105: } +105: match = { +105: 0,0}, +105: 1,1}, +105: 2,2}, +105: 3,4}, +105: 4,5}, +105: 5,6}, +105: 6,7}, +105: 7,8}, +105: 8,9}, +105: 9,14}, +105: 10,15}, +105: 11,16}, +105: } +87: [02:43:48] Explicit valence for atom # 27 P, 6, is greater than permitted +102: Finished +102: ----------------------- +102: testRootedSubgraphs +102: Finished +102: ----------------------- +102: testRootedPaths +102: Finished + 96/230 Test #102: testSubgraphs1 ......................... Passed 1.00 sec +test 106 + Start 106: pyFilterCatalog - BMS-986142_3d.cxsmi +106: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +106: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +106: Test timeout computed to be: 1500 + 97/230 Test #105: filterCatalogTest ...................... Passed 0.76 sec +test 107 + Start 107: testFragCatalog -=============================================================================== -test cases: 29 | 28 passed | 1 failed -assertions: 2445 | 2444 passed | 1 failed +107: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog +107: Test timeout computed to be: 1500 +107: 21 + 98/230 Test #106: pyFilterCatalog ........................***Exception: SegFault 0.79 sec +test 108 + Start 108: pyFragCatalog -test 120 - Start 120: testGETAWAY +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap +108: Test timeout computed to be: 1500 + 99/230 Test #108: pyFragCatalog ..........................***Exception: SegFault 0.65 sec -120: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -120: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [06:21:45] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] Empty atom list: 'M ALS 1 0 F' on line 8. -113: 400 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: de_DE.UTF-8 -68: [06:21:45] ------------------------------------- -68: [06:21:45] Test multithreading Locale Switching -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [06:21:45] ------------------------------------- -112: [06:21:45] Test empty molecule BCUT. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 99/230 Test #112: testBCUT ............................... Passed 0.74 sec -test 121 - Start 121: testAUTOCORR3D +test 109 + Start 109: testDescriptors -121: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors -121: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] Test multithreading (Done) -68: [06:21:45] ------------------------------------- -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: *************************************** -68: *************************************** -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [06:21:45] bond with order 0 found on line 7. This is not part of the MDL specification. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -107: [06:21:45] +109: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +109: Test timeout computed to be: 1500 +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Crippen parameter acquisition. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Crippen calculation. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Issue262: problems with Crippen calculation from pickles. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test AMW calculation. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Exact MW calculation. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Labute ASA descriptors. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test TPSA descriptors. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Lipinski parameters. +87: [02:43:50] Explicit valence for atom # 9 N, 6, is greater than permitted +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test VSA descriptors. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test molecular formula calculation. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Issue 3415534. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test Issue3433771: Bad definition for Crippen atom type O11. +109: [02:43:50] done +109: [02:43:50] ------------------------------------- +109: [02:43:50] Test multithreading +109: reading molecules +109: processing +109: launch :0 +109: launch :1 +109: launch :2 +109: launch :3 +87: [02:43:51] Explicit valence for atom # 3 Al, 6, is greater than permitted +107: [02:43:51] 107: 107: **** 107: Invariant Violation @@ -26193,17 +25748,17 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0xF7F31C36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0xF7F3DC36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x56640C24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x5663D6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0xF74E5D43 in /lib/i386-linux-gnu/libc.so.6 +107: 4# 0x565BDC24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x565BA6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0xF74DED43 in /lib/i386-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -107: 8# 0x5663D7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x565BA7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: -107: [06:21:45] +107: [02:43:51] 107: 107: **** 107: Invariant Violation @@ -26214,17 +25769,17 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0xF7F31C36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0xF7F3DC36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x56640C24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x5663D6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0xF74E5D43 in /lib/i386-linux-gnu/libc.so.6 +107: 4# 0x565BDC24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x565BA6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0xF74DED43 in /lib/i386-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -107: 8# 0x5663D7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x565BA7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: -107: [06:21:45] +107: [02:43:51] 107: 107: **** 107: Invariant Violation @@ -26235,120 +25790,937 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0xF7F31C36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0xF7F3DC36 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x56640C24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x5663D6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0xF74E5D43 in /lib/i386-linux-gnu/libc.so.6 +107: 4# 0x565BDC24 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x565BA6BB in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0xF74DED43 in /lib/i386-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -107: 8# 0x5663D7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x565BA7E7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100/230 Test #107: testFragCatalog ........................ Passed 1.00 sec +100/230 Test #107: testFragCatalog ........................ Passed 2.10 sec +test 110 + Start 110: testAUTOCORR2D + +110: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +110: Test timeout computed to be: 1500 +110: [02:43:51] ---------------------------- +110: start test autocorr2D +87: [02:43:51] Explicit valence for atom # 4 Al, 6, is greater than permitted +87: [02:43:51] Explicit valence for atom # 10 Si, 6, is greater than permitted +110: [02:43:52] done +110: [02:43:52] ------------------------------------- +110: [02:43:52] Test Github #3806: NaNs from AUTOCORR2D descriptor +110: [02:43:52] done +101/230 Test #110: testAUTOCORR2D ......................... Passed 0.76 sec +test 111 + Start 111: testATF + +111: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF +111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 +102/230 Test #111: testATF ................................ Passed 0.08 sec +test 112 + Start 112: testBCUT + +112: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT +112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +112: Test timeout computed to be: 1500 +112: [02:43:52] ------------------------------------- +112: [02:43:52] Basic BCUT tests. +112: [02:43:52] done +112: [02:43:52] ------------------------------------- +112: [02:43:52] Larger BCUT tests. +87: [02:43:52] Explicit valence for atom # 2 O, 4, is greater than permitted +87: [02:43:52] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [02:43:52] Explicit valence for atom # 3 Be, 4, is greater than permitted +87: [02:43:52] Explicit valence for atom # 27 P, 6, is greater than permitted +87: =============================================================================== +87: All tests passed (21162 assertions in 3 test cases) +87: +103/230 Test #87: multithreadedSupplierCatchTest ......... Passed 10.60 sec +test 113 + Start 113: testEEM + +113: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM +113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +113: =>start test EEM +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 0 +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [02:43:53] ------------------------------------- +112: [02:43:53] Test empty molecule BCUT. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104/230 Test #112: testBCUT ............................... Passed 1.05 sec +test 114 + Start 114: testPBF + +114: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF +114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [02:43:53] ------------------------------------- +114: [02:43:53] Basic PBF tests. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 100 +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [02:43:53] done +114: [02:43:53] ------------------------------------- +114: [02:43:53] PBF edge cases. +114: [02:43:53] done +105/230 Test #114: testPBF ................................ Passed 0.41 sec +test 115 + Start 115: testRDFcustom + +115: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 200 +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [02:43:54] Finished: testSmiCorrectness() +73: [02:43:54] ----------------------------------------- +73: +73: [02:43:54] +73: ----------------------------------------- +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 300 +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [02:43:54] Spurious data before the first property will be ignored +73: [02:43:54] Property will be truncated after the first blank line +73: [02:43:54] Property will be truncated after the first blank line +73: [02:43:54] Property will be truncated after the first blank line +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 400 +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [02:43:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: Elapsed time: 2.43298 s +113: Errors:0 +113: [02:43:55] test on : 500 molecules done +106/230 Test #113: testEEM ................................ Passed 2.50 sec +test 116 + Start 116: testRDF + +116: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF +116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +73: [02:43:55] Finished: testSDCorrectness() +73: [02:43:55] ----------------------------------------- +73: +107/230 Test #73: testMultithreadedMolSupplier ........... Passed 14.75 sec +test 117 + Start 117: testMORSE + +117: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE +117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test Issue252: Bad definitions for Crippen atom types. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of ChiVs. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of ChiNs. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of HallKierAlpha. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of Kappa1. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of Kappa2. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of Kappa3. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test Crippen atom type calculations. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test ring descriptors +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test other count descriptors. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test MQN +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test GitHub Issue 56. +109: [02:43:56] WARNING: not removing hydrogen atom without neighbors +109: [02:43:56] WARNING: not removing hydrogen atom without neighbors +109: [02:43:56] WARNING: not removing hydrogen atom without neighbors +109: [02:43:56] WARNING: not removing hydrogen atom without neighbors +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test Github92: Bad Crippen atom type for pyrrole H. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test Github362: order dependence in Kier-Hall descriptors. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test calculation of spiro and bridgehead counts. +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Test Github694: ExactMolWt ignoring the mass of the electron +109: [02:43:56] done +109: [02:43:56] ------------------------------------- +109: [02:43:56] Testing Properties and KitchenSink +109: [02:43:56] ---Caught keyerror (bad property name)--- +109: [02:43:56] +109: +109: **** +109: Test Assert +109: Expression Failed: +109: Violation occurred on line 1971 in file ./Code/GraphMol/Descriptors/test.cpp +109: Failed Expression: pq->Match(*mol) +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x565A6417 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +109: 3# 0x5659E5F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +109: 4# 0xF7486D43 in /lib/i386-linux-gnu/libc.so.6 +109: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 +109: 6# 0x5659EAD7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +109: ---------- +109: **** +109: +109: terminate called after throwing an instance of 'Invar::Invariant' +109: what(): Expression Failed: +108/230 Test #109: testDescriptors ........................Subprocess aborted***Exception: 5.76 sec +[02:43:50] ------------------------------------- +[02:43:50] Test Crippen parameter acquisition. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Crippen calculation. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Issue262: problems with Crippen calculation from pickles. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test AMW calculation. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Exact MW calculation. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Labute ASA descriptors. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test TPSA descriptors. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Lipinski parameters. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test VSA descriptors. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test molecular formula calculation. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Issue 3415534. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test Issue3433771: Bad definition for Crippen atom type O11. +[02:43:50] done +[02:43:50] ------------------------------------- +[02:43:50] Test multithreading +reading molecules +processing + launch :0 + launch :1 + launch :2 + launch :3 +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test Issue252: Bad definitions for Crippen atom types. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of ChiVs. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of ChiNs. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of HallKierAlpha. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of Kappa1. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of Kappa2. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of Kappa3. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test Crippen atom type calculations. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test ring descriptors +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test other count descriptors. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test MQN +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test GitHub Issue 56. +[02:43:56] WARNING: not removing hydrogen atom without neighbors +[02:43:56] WARNING: not removing hydrogen atom without neighbors +[02:43:56] WARNING: not removing hydrogen atom without neighbors +[02:43:56] WARNING: not removing hydrogen atom without neighbors +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test Github92: Bad Crippen atom type for pyrrole H. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test Github362: order dependence in Kier-Hall descriptors. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test calculation of spiro and bridgehead counts. +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Test Github694: ExactMolWt ignoring the mass of the electron +[02:43:56] done +[02:43:56] ------------------------------------- +[02:43:56] Testing Properties and KitchenSink +[02:43:56] ---Caught keyerror (bad property name)--- +[02:43:56] + +**** +Test Assert +Expression Failed: +Violation occurred on line 1971 in file ./Code/GraphMol/Descriptors/test.cpp +Failed Expression: pq->Match(*mol) +---------- +Stacktrace: + 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 + 2# 0x565A6417 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors + 3# 0x5659E5F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors + 4# 0xF7486D43 in /lib/i386-linux-gnu/libc.so.6 + 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 + 6# 0x5659EAD7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +---------- +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + +test 118 + Start 118: test3D + +118: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D +118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +118: [02:43:56] ------------------------------------- +118: [02:43:56] Basic PMI tests. +115: =>start test rdf custom +115: [02:43:56] test on : 365 molecules done +79: =============================================================================== +79: All tests passed (1586 assertions in 98 test cases) +79: +109/230 Test #79: fileParsersCatchTest ................... Passed 14.62 sec +test 119 + Start 119: testWHIM + +119: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testWHIM +119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] More PMI/NPR tests. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] Basic NPR tests. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] PMI edge cases. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] NPR edge cases. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] 3D descriptors. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] 3D descriptor edge cases. +118: [02:43:56] done +118: [02:43:56] ------------------------------------- +118: [02:43:56] Inertial shape factor. +118: [02:43:56] done +119: =>start test WHIM +119: [02:43:56] test on : 365 molecules done +110/230 Test #118: test3D ................................. Passed 0.86 sec +test 120 + Start 120: testGETAWAY + +120: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +120: Test timeout computed to be: 1500 +111/230 Test #119: testWHIM ............................... Passed 0.65 sec +test 121 + Start 121: testAUTOCORR3D + +121: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors +121: Test timeout computed to be: 1500 +117: =>start test MORSE +117: =>read file +117: [02:43:57] test on : 365 molecules done +112/230 Test #117: testMORSE .............................. Passed 1.68 sec test 122 Start 122: testCoulombMat 122: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 122: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [06:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: Elapsed time: 0.774085 s -113: Errors:0 -113: [06:21:45] test on : 500 molecules done -68: [06:21:45] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [06:21:45] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [06:21:45] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -101/230 Test #113: testEEM ................................ Passed 0.82 sec +122: ===================== Testing CoulombMat ======================= +122: CM test 1 mat Done +113/230 Test #122: testCoulombMat ......................... Passed 0.05 sec test 123 Start 123: descriptorsTestCatch 123: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 123: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -68: generating smiles -68: 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 -68: converting back -122: ===================== Testing CoulombMat ======================= -68: check isomorphism -119: =>start test WHIM -119: [06:21:45] test on : 365 molecules done -102/230 Test #119: testWHIM ............................... Passed 0.47 sec +123: Randomness seeded to: 114799050 +123: Warning: Atom Count for residue GLU5A does not match expected count +123: Warning: Atom Count for residue ASN39A does not match expected count +123: Warning: Atom Count for residue GLU53A does not match expected count +123: Warning: Atom Count for residue ARG64A does not match expected count +123: Warning: Atom Count for residue LYS80A does not match expected count +116: =>start test rdf +116: [02:43:57] test on : 365 molecules done +114/230 Test #116: testRDF ................................ Passed 2.01 sec test 124 Start 124: pyMolDescriptors 124: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 124: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 124: Test timeout computed to be: 1500 -122: CM test 1 mat Done -103/230 Test #122: testCoulombMat ......................... Passed 0.08 sec +123: Warning: Atom Count for residue GLU150A does not match expected count +123: Warning: Atom Count for residue ASN157A does not match expected count +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +121: =>start test autocorr3D +121: [02:43:57] test on : 365 molecules done +115/230 Test #121: testAUTOCORR3D ......................... Passed 0.71 sec test 125 Start 125: pyMolDescriptors3D 125: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/test3D.py" 125: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 125: Test timeout computed to be: 1500 -118: [06:21:45] done -118: [06:21:45] ------------------------------------- -118: [06:21:45] More PMI/NPR tests. -118: [06:21:45] done -118: [06:21:45] ------------------------------------- -118: [06:21:45] Basic NPR tests. -123: Randomness seeded to: 3541453900 123: Warning: Atom Count for residue GLU5A does not match expected count -123: Warning: Atom Count for residue ASN39A does not match expected count -123: Warning: Atom Count for residue GLU53A does not match expected count -123: Warning: Atom Count for residue ARG64A does not match expected count -123: Warning: Atom Count for residue LYS80A does not match expected count -123: Warning: Atom Count for residue GLU150A does not match expected count -123: Warning: Atom Count for residue ASN157A does not match expected count -118: [06:21:46] done -118: [06:21:46] ------------------------------------- -118: [06:21:46] PMI edge cases. -118: [06:21:46] done -118: [06:21:46] ------------------------------------- -118: [06:21:46] NPR edge cases. -118: [06:21:46] done -118: [06:21:46] ------------------------------------- -118: [06:21:46] 3D descriptors. -118: [06:21:46] done -118: [06:21:46] ------------------------------------- -118: [06:21:46] 3D descriptor edge cases. -118: [06:21:46] done -118: [06:21:46] ------------------------------------- -118: [06:21:46] Inertial shape factor. -118: [06:21:46] done -104/230 Test #118: test3D ................................. Passed 0.82 sec +27: All 191 tests passed +115: =>start test morse custom +115: [02:43:57] test on : 365 molecules done +116/230 Test #124: pyMolDescriptors .......................***Exception: SegFault 0.37 sec + test 126 Start 126: testFingerprints 126: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 126: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 126: Test timeout computed to be: 1500 -105/230 Test #125: pyMolDescriptors3D .....................***Exception: SegFault 0.33 sec - -test 127 - Start 127: testMHFPFingerprint - -127: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints -127: Test timeout computed to be: 1500 -106/230 Test #124: pyMolDescriptors .......................***Exception: SegFault 0.36 sec - -test 128 - Start 128: testFingerprintGenerators - -128: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -127: [06:21:46] ------------------------------------- -127: [06:21:46] Test MHFP fingerprint encoder initialization 126: 126: 126: @@ -26478,6 +26850,8 @@ 126: 126: ------------------- 126: +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 126: SMI: c1c(O)nc(O)c2c1[nH]cn2 126: Atoms: 126: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 @@ -26514,8 +26888,6 @@ 126: 126: 126: ------------------- -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test atom-pair fp generator 126: 126: SMI: c12cc(O)nc(O)c1nc[nH]2 126: Atoms: @@ -26747,17 +27119,6 @@ 126: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 126: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 126: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -123: Warning: Atom Count for residue GLU5A does not match expected count -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test atom-pair fp generator with different arguments -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator 126: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 126: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 126: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 @@ -26845,168 +27206,544 @@ 126: 126: ------------------- 126: -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -127: [06:21:46] done -127: [06:21:46] ------------------------------------- -127: [06:21:46] Test MHFP shingling creation -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test atom-pair additional output -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Folded Atom Pairs. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Rooted Atom Pairs. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test ignoring atoms in Atom Pairs. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Atom Pairs including info about chirality. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Morgan Fingerprints. -87: [06:21:46] Explicit valence for atom # 9 N, 6, is greater than permitted -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test morgan fp generator -121: =>start test autocorr3D -121: [06:21:46] test on : 365 molecules done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Morgan Fingerprints. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Morgan Fingerprints using fromAtoms argument. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Morgan Fingerprints as bit vects. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Morgan Fingerprints with feature invariants. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test additional Morgan fingerprints options. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Atom Codes. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Atom Pairs. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Atom Pairs part 2. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Topological Torsions. -107/230 Test #121: testAUTOCORR3D ......................... Passed 0.58 sec +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Morgan Fingerprints. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Morgan Fingerprints using fromAtoms argument. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Morgan Fingerprints as bit vects. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Morgan Fingerprints with feature invariants. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test additional Morgan fingerprints options. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Atom Codes. +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Atom Pairs. +126: [02:43:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Atom Pairs part 2. +126: [02:43:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Topological Torsions. +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] done +126: [02:43:57] ------------------------------------- +126: [02:43:57] Test Bulk Topological Torsions. +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +117/230 Test #125: pyMolDescriptors3D .....................***Exception: SegFault 0.37 sec + +test 127 + Start 127: testMHFPFingerprint + +127: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints +127: Test timeout computed to be: 1500 +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +127: [02:43:58] ------------------------------------- +127: [02:43:58] Test MHFP fingerprint encoder initialization +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +127: [02:43:58] done +127: [02:43:58] ------------------------------------- +127: [02:43:58] Test MHFP shingling creation +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +127: [02:43:58] done +127: [02:43:58] ------------------------------------- +127: [02:43:58] Test MHFP hashing of string and uint arrays +127: [02:43:58] done +127: [02:43:58] ------------------------------------- +127: [02:43:58] Test SECFP fingerprint functionality +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +127: [02:43:58] done +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +118/230 Test #127: testMHFPFingerprint .................... Passed 0.13 sec +test 128 + Start 128: testFingerprintGenerators + +128: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test atom-pair fp generator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Hashed Atom Pairs. +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Hashed torsions. +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Rooted Atom Pairs. +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test ignoring atoms in Atom Pairs. +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Rooted Topological Torsions. +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test ignoring atoms in Topological Torsions. +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test atom info from morgan fingerprints. +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test atom info from morgan fingerprints including Info Redundant Environments. +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] ------------------------------------- +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +123: Warning: Atom Count for residue ASN39A does not match expected count +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] ------------------------------------- +126: [02:43:58] ------------------------------------- +126: [02:43:58] ------------------------------------- +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Atom Pairs including info about chirality. +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test Topological Torsions including info about chirality. +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test GitHub Issue 25: fingerprint backwards compatibility. +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test atom-pair fp generator with different arguments +126: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test GitHub Issue 151: PatternFingerprint problems +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test 3D atom pairs. +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +126: [02:43:58] done +126: [02:43:58] ------------------------------------- +126: [02:43:58] Test multithreading with the pattern FP +126: reading molecules +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] DEPRECATION WARNING: please use AtomPairGenerator +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test atom-pair additional output +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Folded Atom Pairs. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Rooted Atom Pairs. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test ignoring atoms in Atom Pairs. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Atom Pairs including info about chirality. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Morgan Fingerprints. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test morgan fp generator +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Morgan Fingerprints using fromAtoms argument. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Morgan Fingerprints as bit vects. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Morgan Fingerprints with feature invariants. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test additional Morgan fingerprints options. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Single atoms setting radius 1 bits in Morgan fingerprints +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test different invariant generator combinations +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test invariant overriding +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test RDKit fp generator +126: pass 1 +126: launch :0 +126: launch :1 +126: launch :2 +126: launch :3 +123: Warning: Atom Count for residue GLU53A does not match expected count +123: Warning: Atom Count for residue ARG64A does not match expected count +126: pass 2 +126: launch :0 +126: launch :1 +126: launch :2 +126: launch :3 +115: =>start test AUTOCORR3D custom +115: [02:43:58] test on : 365 molecules done +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test unfolded version of RDKFP +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test topological torsion fp generator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Topological Torsions. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Folded torsions. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Bulk Topological Torsions. +123: Warning: Atom Count for residue LYS80A does not match expected count +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Rooted Topological Torsions. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test ignoring atoms in Topological Torsions. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test Topological Torsions including info about chirality. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [02:43:58] done +128: [02:43:58] ------------------------------------- +128: [02:43:58] Test convenience and bulk fp calculation functions +115: =>start test 2 WHIM custom +115: [02:43:59] test on : 365 molecules done +128: [02:43:59] done +128: [02:43:59] ------------------------------------- +128: [02:43:59] Test GitHub Issue #6958 +128: [02:43:59] DEPRECATION WARNING: please use AtomPairGenerator +119/230 Test #128: testFingerprintGenerators .............. Passed 1.40 sec test 129 Start 129: fpTestCatch 129: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 129: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Bulk Topological Torsions. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: [06:21:46] done -127: [06:21:46] ------------------------------------- -127: [06:21:46] Test MHFP hashing of string and uint arrays -127: [06:21:46] done -127: [06:21:46] ------------------------------------- -127: [06:21:46] Test SECFP fingerprint functionality -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Morgan Fingerprints using fromAtoms argument. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Morgan Fingerprints as bit vects. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Morgan Fingerprints with feature invariants. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test additional Morgan fingerprints options. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Single atoms setting radius 1 bits in Morgan fingerprints -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test different invariant generator combinations -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test invariant overriding -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test RDKit fp generator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117: =>start test MORSE -117: =>read file -117: [06:21:46] test on : 365 molecules done -108/230 Test #117: testMORSE .............................. Passed 1.02 sec -test 130 - Start 130: fpGenTestCatch - -130: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch -130: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints -130: Test timeout computed to be: 1500 -127: [06:21:46] done -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -109/230 Test #127: testMHFPFingerprint .................... Passed 0.12 sec -test 131 - Start 131: pyTestGenerator - -131: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" -131: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap -131: Test timeout computed to be: 1500 -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: Randomness seeded to: 1816068245 +129: Randomness seeded to: 2356872996 129: 129: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129: fpTestCatch is a Catch2 v3.7.1 host application. @@ -27043,17 +27780,12 @@ 129: 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 30073176097 129: (0x700804021) } } 129: -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator 129: =============================================================================== 129: test cases: 16 | 15 passed | 1 failed 129: assertions: 188 | 186 passed | 2 failed 129: -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -110/230 Test #129: fpTestCatch ............................***Failed 0.05 sec -Randomness seeded to: 1816068245 +120/230 Test #129: fpTestCatch ............................***Failed 0.12 sec +Randomness seeded to: 2356872996 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fpTestCatch is a Catch2 v3.7.1 host application. @@ -27095,372 +27827,59 @@ assertions: 188 | 186 passed | 2 failed +test 130 + Start 130: fpGenTestCatch + +130: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch +130: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints +130: Test timeout computed to be: 1500 +115: =>start test 1 WHIM custom +115: [02:43:59] test on : 365 molecules done +123: Warning: Atom Count for residue GLU150A does not match expected count +130: Randomness seeded to: 1505521362 +130: =============================================================================== +130: All tests passed (2692 assertions in 5 test cases) +130: +121/230 Test #130: fpGenTestCatch ......................... Passed 0.24 sec +test 131 + Start 131: pyTestGenerator + +131: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" +131: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap +131: Test timeout computed to be: 1500 +123: Warning: Atom Count for residue ASN157A does not match expected count +122/230 Test #131: pyTestGenerator ........................***Exception: SegFault 0.42 sec + test 132 Start 132: pyTestMHFP 132: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 132: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 132: Test timeout computed to be: 1500 -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -87: [06:21:46] Explicit valence for atom # 3 Al, 6, is greater than permitted -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -87: [06:21:46] Explicit valence for atom # 4 Al, 6, is greater than permitted -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -87: [06:21:46] Explicit valence for atom # 10 Si, 6, is greater than permitted -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Hashed Atom Pairs. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Hashed torsions. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Rooted Atom Pairs. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test ignoring atoms in Atom Pairs. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Rooted Topological Torsions. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test ignoring atoms in Topological Torsions. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test atom info from morgan fingerprints. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test atom info from morgan fingerprints including Info Redundant Environments. -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -130: Randomness seeded to: 2527978138 -130: =============================================================================== -130: All tests passed (2692 assertions in 5 test cases) -130: -111/230 Test #130: fpGenTestCatch ......................... Passed 0.29 sec +123/230 Test #132: pyTestMHFP .............................***Exception: SegFault 0.36 sec + test 133 Start 133: testPartialCharges 133: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 133: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges 133: Test timeout computed to be: 1500 -126: [06:21:46] ------------------------------------- -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] ------------------------------------- -126: [06:21:46] ------------------------------------- -126: [06:21:46] ------------------------------------- -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Atom Pairs including info about chirality. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test Topological Torsions including info about chirality. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test GitHub Issue 25: fingerprint backwards compatibility. -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test GitHub Issue 151: PatternFingerprint problems -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test 3D atom pairs. -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -126: [06:21:46] done -126: [06:21:46] ------------------------------------- -126: [06:21:46] Test multithreading with the pattern FP -126: reading molecules -112/230 Test #133: testPartialCharges ..................... Passed 0.07 sec +124/230 Test #133: testPartialCharges ..................... Passed 0.08 sec test 134 Start 134: pyPartialCharges 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap 134: Test timeout computed to be: 1500 -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test unfolded version of RDKFP -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test topological torsion fp generator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Topological Torsions. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Folded torsions. -126: pass 1 -126: launch :0 -126: launch :1 -126: launch :2 -126: launch :3 -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Bulk Topological Torsions. -113/230 Test #132: pyTestMHFP .............................***Exception: SegFault 0.37 sec - +120: =>start test GETAWAY +120: [02:44:00] test on : 365 molecules done +125/230 Test #120: testGETAWAY ............................ Passed 4.04 sec test 135 Start 135: testMolTransforms 135: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 135: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 135: Test timeout computed to be: 1500 -114/230 Test #131: pyTestGenerator ........................***Exception: SegFault 0.42 sec - -test 136 - Start 136: molTransformsTestCatch - -136: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms -136: Test timeout computed to be: 1500 135: *********************************************************** 135: Testing MolTransforms 135: --------------------------------- @@ -27491,79 +27910,44 @@ 135: testWeightedCentroid 135: 135: *********************************************************** -115/230 Test #135: testMolTransforms ...................... Passed 0.10 sec +126/230 Test #135: testMolTransforms ...................... Passed 0.17 sec +test 136 + Start 136: molTransformsTestCatch + +136: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms +136: Test timeout computed to be: 1500 +136: Randomness seeded to: 39519641 +136: =============================================================================== +136: All tests passed (4 assertions in 1 test case) +136: +127/230 Test #136: molTransformsTestCatch ................. Passed 0.05 sec test 137 Start 137: pyMolTransforms 137: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 137: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap 137: Test timeout computed to be: 1500 -136: Randomness seeded to: 3505729020 -136: =============================================================================== -136: All tests passed (4 assertions in 1 test case) -136: -116/230 Test #136: molTransformsTestCatch ................. Passed 0.09 sec +50: Randomness seeded to: 4182454430 +50: =============================================================================== +50: All tests passed (14835 assertions in 14 test cases) +50: +128/230 Test #50: canonTestsCatch ........................ Passed 26.54 sec test 138 Start 138: forceFieldHelpersCatch 138: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 138: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers 138: Test timeout computed to be: 1500 -68: [06:21:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [06:21:46] deprecated group abbreviation ignored on line 24 -68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -68: [06:21:46] -68: -68: **** -68: Post-condition Violation -68: Element 'Mv' not found -68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -68: Failed Expression: anum > -1 -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0xF7DADCC8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0xF7DB75D0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 7# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 8# 0x565B7F80 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 9# 0x5662AE79 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x5659CC93 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0xF746CD43 in /lib/i386-linux-gnu/libc.so.6 -68: 12# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -68: 13# 0x5659CDB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Rooted Topological Torsions. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test ignoring atoms in Topological Torsions. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test Topological Torsions including info about chirality. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [06:21:46] done -128: [06:21:46] ------------------------------------- -128: [06:21:46] Test convenience and bulk fp calculation functions -138: Randomness seeded to: 1384213041 +129/230 Test #134: pyPartialCharges .......................***Exception: SegFault 0.54 sec + +test 139 + Start 139: testMMFFForceFieldHelpers + +139: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +139: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +139: Test timeout computed to be: 1500 +138: Randomness seeded to: 1079894563 138: 138: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 138: forceFieldHelpersCatch is a Catch2 v3.7.1 host application. @@ -27585,8 +27969,8 @@ 138: test cases: 1 | 0 passed | 1 failed 138: assertions: 11 | 10 passed | 1 failed 138: -117/230 Test #138: forceFieldHelpersCatch .................***Failed 0.05 sec -Randomness seeded to: 1384213041 +130/230 Test #138: forceFieldHelpersCatch .................***Failed 0.11 sec +Randomness seeded to: 1079894563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ forceFieldHelpersCatch is a Catch2 v3.7.1 host application. @@ -27609,133 +27993,19 @@ assertions: 11 | 10 passed | 1 failed -test 139 - Start 139: testMMFFForceFieldHelpers - -139: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -139: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -139: Test timeout computed to be: 1500 -139: [06:21:46] ------------------------------------- -139: [06:21:46] Test MMFF atom types. -139: [06:21:46] done -139: [06:21:46] ------------------------------------- -139: [06:21:46] Testing MMFF builder tools. -87: [06:21:46] Explicit valence for atom # 2 O, 4, is greater than permitted -139: [06:21:46] done -139: [06:21:46] ------------------------------------- -139: [06:21:46] Testing MMFF builder+minimization. -123: Warning: Atom Count for residue ASN39A does not match expected count -126: pass 2 -126: launch :0 -126: launch :1 -126: launch :2 -126: launch :3 -87: [06:21:46] Explicit valence for atom # 3 Al, 6, is greater than permitted -39: [06:21:46] done: 500000 -39: [06:21:46] Done -87: [06:21:46] Explicit valence for atom # 3 Be, 4, is greater than permitted -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -139: [06:21:46] done -139: [06:21:46] ------------------------------------- -139: [06:21:46] Testing Issue239. -118/230 Test #134: pyPartialCharges .......................***Exception: SegFault 0.38 sec - test 140 Start 140: testMMFFForceFieldHelpersMultiThread 140: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 140: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 140: Test timeout computed to be: 1500 -39: [06:21:47] Testing hanoi with a functor. -39: [06:21:47] Done -39: [06:21:47] Testing basic partition refinement. -39: [06:21:47] Done -39: [06:21:47] Testing partition refinement with neighbors. -39: [06:21:47] Done -39: [06:21:47] testing canonicalization via tie breaking. -39: [06:21:47] Done -39: [06:21:47] testing canonicalization using the wrapper. -68: [06:21:47] 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: [06:21:47] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -39: [06:21:47] Done -39: [06:21:47] testing some specific ordering problems -39: [06:21:47] Finished -39: [06:21:47] testing chiral invariants. -39: [06:21:47] Finished -39: [06:21:47] testing unique ranks in w.r.t. renumbering. -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing calcEnergy with passed coords. -123: Warning: Atom Count for residue GLU53A does not match expected count -140: [06:21:47] ------------------------------------- -140: [06:21:47] Test MMFF multithreading -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing calcGrad. -119/230 Test #137: pyMolTransforms ........................***Exception: SegFault 0.30 sec - -test 141 - Start 141: testUFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -141: Test timeout computed to be: 1500 -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing Issue242. -39: [06:21:47] Finished -39: [06:21:47] testing mol fragments. -39: [06:21:47] Finished -39: [06:21:47] testing protein round-tripping. -141: [06:21:47] ------------------------------------- -141: [06:21:47] Test UFF atom labels. -123: Warning: Atom Count for residue ARG64A does not match expected count -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing github 308: crash during MMFF parameterization . -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing SFIssue1653802. -68: ---------------------------------- -68: ---------------------------------- -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Testing SFIssue2378119. -139: [06:21:47] done -139: [06:21:47] ------------------------------------- -139: [06:21:47] Test MMFF force-field parameter getters. -139: [06:21:47] ------------------------------------- -139: [06:21:47] Test MMFF multithreading -68: [06:21:47] -68: -68: **** -68: Pre-condition Violation -68: rlabel out of range for MDL files -68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -68: Failed Expression: rlabel >= 0 && rlabel < 100 -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x565C7582 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x5662AEF1 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x5659CC93 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0xF746CD43 in /lib/i386-linux-gnu/libc.so.6 -68: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -68: 8# 0x5659CDB7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -68: [06:21:47] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Test UFF atom typer. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing UFF builder tools. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing UFF builder+minimization. +140: [02:44:01] ------------------------------------- +140: [02:44:01] Test MMFF multithreading +139: [02:44:01] ------------------------------------- +139: [02:44:01] Test MMFF atom types. +139: [02:44:01] done +139: [02:44:01] ------------------------------------- +139: [02:44:01] Testing MMFF builder tools. 140: processing 140: launch :0 140: launch :1 @@ -27761,244 +28031,528 @@ 140: launch :21 140: launch :22 140: launch :23 -139: generating reference data -87: [06:21:47] Explicit valence for atom # 27 P, 6, is greater than permitted -27: All 191 tests passed -123: Warning: Atom Count for residue LYS80A does not match expected count -87: =============================================================================== -87: All tests passed (21162 assertions in 3 test cases) -87: -120/230 Test #87: multithreadedSupplierCatchTest ......... Passed 3.42 sec +139: [02:44:01] done +139: [02:44:01] ------------------------------------- +139: [02:44:01] Testing MMFF builder+minimization. +131/230 Test #137: pyMolTransforms ........................***Exception: SegFault 0.38 sec + +test 141 + Start 141: testUFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +141: Test timeout computed to be: 1500 +141: [02:44:01] ------------------------------------- +141: [02:44:01] Test UFF atom labels. +141: [02:44:01] done +141: [02:44:01] ------------------------------------- +141: [02:44:01] Test UFF atom typer. +141: [02:44:01] done +141: [02:44:01] ------------------------------------- +141: [02:44:01] Testing UFF builder tools. +141: [02:44:01] done +141: [02:44:01] ------------------------------------- +141: [02:44:01] Testing UFF builder+minimization. +139: [02:44:01] done +139: [02:44:01] ------------------------------------- +139: [02:44:01] Testing Issue239. +139: [02:44:01] done +139: [02:44:01] ------------------------------------- +139: [02:44:01] Testing calcEnergy with passed coords. +139: [02:44:02] done +139: [02:44:02] ------------------------------------- +139: [02:44:02] Testing calcGrad. +140: done +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing UFF special cases. +141: [02:44:02] UFFTYPER: Unrecognized charge state for atom: 0 +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing Issue239. +139: [02:44:02] done +139: [02:44:02] ------------------------------------- +139: [02:44:02] Testing Issue242. +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing calcEnergy with passed coords. +140: [02:44:02] done +132/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.80 sec test 142 Start 142: testCrystalForceField 142: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 142: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 142: Test timeout computed to be: 1500 -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +139: [02:44:02] done +139: [02:44:02] ------------------------------------- +139: [02:44:02] Testing github 308: crash during MMFF parameterization . +139: [02:44:02] ------------------------------------- +139: [02:44:02] Testing SFIssue1653802. +139: [02:44:02] done +139: [02:44:02] ------------------------------------- +139: [02:44:02] Testing SFIssue2378119. +139: [02:44:02] done +139: [02:44:02] ------------------------------------- +139: [02:44:02] Test MMFF force-field parameter getters. +139: [02:44:02] ------------------------------------- +139: [02:44:02] Test MMFF multithreading +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing calcGrad. +139: generating reference data 142: ------------------------------------- 142: Test CrystalFF torsional term. -128: [06:21:47] done -128: [06:21:47] ------------------------------------- -128: [06:21:47] Test GitHub Issue #6958 -128: [06:21:47] DEPRECATION WARNING: please use AtomPairGenerator -121/230 Test #128: testFingerprintGenerators .............. Passed 1.31 sec +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing SFIssue1653802. +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing SFIssue2378119. +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Test UFF force-field parameter getters. +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing handling missing parameters. +141: [02:44:02] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [02:44:02] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [02:44:02] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [02:44:02] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Testing SFIssue3009337. +141: [02:44:02] done +141: [02:44:02] ------------------------------------- +141: [02:44:02] Test UFF multithreading +141: generating reference data +133/230 Test #142: testCrystalForceField .................. Passed 0.35 sec test 143 Start 143: pyForceFieldHelpers 143: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 143: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 143: Test timeout computed to be: 1500 -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing UFF special cases. -141: [06:21:47] UFFTYPER: Unrecognized charge state for atom: 0 -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing Issue239. -68: [06:21:47] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [06:21:47] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing calcEnergy with passed coords. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing calcGrad. -68: [06:21:47] Empty atom list: 'M ALS 1 0 F' on line 8. -122/230 Test #68: fileParsersTest1 ....................... Passed 3.91 sec +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [02:44:03] [02:44:03] Rep: 0 Mol:1 +141: Rep: 0 Mol:3[02:44:03] Rep: 0 Mol:0 +141: +141: [02:44:03] Rep: 0 Mol:2 +141: [02:44:03] Rep: 0 Mol:5 +141: [02:44:03] Rep: 0 Mol:9 +141: [02:44:03] Rep: 0 Mol:4 +141: [02:44:03] Rep: 0 Mol:7 +141: [02:44:03] Rep: 0 Mol:11 +141: [02:44:03] Rep: 0 Mol:13 +141: [02:44:03] Rep: 0 Mol:15 +141: [02:44:03] Rep: 0 Mol:19 +141: [02:44:03] Rep: 0 Mol:6 +141: [02:44:03] Rep: 0 Mol:23 +141: [02:44:03] Rep: 0 Mol:27 +134/230 Test #143: pyForceFieldHelpers ....................***Exception: SegFault 0.59 sec + test 144 Start 144: testDistGeomHelpers 144: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 144: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 144: Test timeout computed to be: 1500 -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing SFIssue1653802. -39: [06:21:47] Finished -39: [06:21:47] testing stability w.r.t. renumbering. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing SFIssue2378119. -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Test UFF force-field parameter getters. -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing handling missing parameters. -141: [06:21:47] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [06:21:47] UFFTYPER: Unrecognized atom type: Cu+1 (0) -141: [06:21:47] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [06:21:47] UFFTYPER: Unrecognized atom type: Cu+1 (0) -140: done -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Testing SFIssue3009337. -144: [06:21:47] ******************************************************** -144: [06:21:47] Testing DistGeomHelpers -144: [06:21:47] --------------------------------- -144: [06:21:47] test2 +141: [02:44:03] Rep: 0 Mol:31 +141: [02:44:03] Rep: 0 Mol:10 +141: [02:44:03] Rep: 0 Mol:17 +141: [02:44:03] Rep: 0 Mol:8 +144: [02:44:03] ******************************************************** +144: [02:44:03] Testing DistGeomHelpers +144: [02:44:03] --------------------------------- +144: [02:44:03] test2 144: 144: go -123/230 Test #142: testCrystalForceField .................. Passed 0.25 sec +141: [02:44:03] Rep: 0 Mol:12 +144: ------------------------------------- +144: +141: [02:44:03] Rep: 0 Mol:16 +141: [02:44:03] Rep: 0 Mol:14 +141: [02:44:03] Rep: 0 Mol:18 +141: [02:44:03] Rep: 0 Mol:21 +141: [02:44:03] Rep: 0 Mol:20 +141: [02:44:03] Rep: 0 Mol:22 +141: [02:44:03] Rep: 0 Mol:26 +141: [02:44:03] Rep: 0 Mol:25 +141: [02:44:03] Rep: 0 Mol:24 +141: [02:44:03] Rep: 0 Mol:28 +141: [02:44:03] Rep: 0 Mol:30 +141: [02:44:03] Rep: 0 Mol:29 +139: processing +139: launch :0 +139: launch :1 +139: [02:44:03] launch :2 +139: Rep: 0 Mol:0 +139: [02:44:03] Rep: 0 Mol:1 +139: launch :3 +139: [02:44:03] Rep: 0 Mol:5 +139: [02:44:03] Rep: 0 Mol:2 +139: [02:44:03] Rep: 0 Mol:3 +139: [02:44:03] Rep: 0 Mol:9 +139: [02:44:03] Rep: 0 Mol:4 +139: [02:44:03] Rep: 0 Mol:13 +139: [02:44:03] Rep: 0 Mol:17 +139: [02:44:03] Rep: 0 Mol:8 +139: [02:44:03] Rep: 0 Mol:6 +139: [02:44:03] Rep: 0 Mol:12 +139: [02:44:03] Rep: 0 Mol:10 +139: [02:44:03] Rep: 0 Mol:16 +141: [02:44:03] Rep: 100 Mol:3 +141: [02:44:03] Rep: 100 Mol:7 +141: [02:44:03] Rep: 100 Mol:11 +141: [02:44:03] Rep: 100 Mol:15 +141: [02:44:03] Rep: 100 Mol:19 +139: [02:44:03] Rep: 0 Mol:21 +141: [02:44:03] Rep: 100 Mol:23 +141: [02:44:03] Rep: 100 Mol:27 +141: [02:44:03] Rep: 100 Mol:31 +139: [02:44:03] Rep: 0 Mol:20 +139: [02:44:03] Rep: 0 Mol:25 +139: [02:44:03] Rep: 0 Mol:24 +139: [02:44:03] Rep: 0 Mol:7 +139: [02:44:03] Rep: 0 Mol:11 +139: [02:44:03] Rep: 0 Mol:29 +139: [02:44:03] Rep: 0 Mol:28 +139: [02:44:03] Rep: 0 Mol:15 +139: [02:44:03] Rep: 0 Mol:19 +139: [02:44:03] Rep: 0 Mol:23 +139: [02:44:03] Rep: 0 Mol:27 +139: [02:44:03] Rep: 0 Mol:31 +139: [02:44:03] Rep: 0 Mol:14 +139: [02:44:04] Rep: 0 Mol:18 +139: [02:44:04] Rep: 0 Mol:22 +139: [02:44:04] Rep: 0 Mol:26 +139: [02:44:04] Rep: 0 Mol:30 +93: 0,0 0 +93: 0,1 0 +93: 1,0 0 +93: 1,1 0 +93: 2,0 0 +93: 2,1 0 +135/230 Test #93: testEnumeration ........................ Passed 19.42 sec test 145 Start 145: distGeomHelpersCatch 145: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 145: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 145: Test timeout computed to be: 1500 -144: ------------------------------------- -144: -140: [06:21:47] done -141: [06:21:47] done -141: [06:21:47] ------------------------------------- -141: [06:21:47] Test UFF multithreading -124/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.69 sec +145: Randomness seeded to: 1510922053 +145: [02:44:04] [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)] +145: [02:44:04] [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)] +139: [02:44:04] Rep: 20 Mol:3 +139: [02:44:04] Rep: 20 Mol:7 +139: [02:44:04] Rep: 20 Mol:11 +139: [02:44:04] Rep: 20 Mol:15 +139: [02:44:04] Rep: 20 Mol:19 +139: [02:44:04] Rep: 20 Mol:23 +139: [02:44:04] Rep: 20 Mol:27 +139: [02:44:04] Rep: 20 Mol:31 +145: [02:44:04] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] 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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [!#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)] +145: [02:44:04] [!#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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: ----------- +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [$([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)] +145: [02:44:04] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [02:44:04] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [02:44:04] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +145: [02:44:04] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +145: ----------- +145: [02:44:04] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$([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)] +145: [02:44:04] [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)] +145: [02:44:04] 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)] +145: ----------- +145: ----------- +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [02:44:04] [$(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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +145: [02:44:04] [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)] +139: [02:44:04] Rep: 20 Mol:0 +139: [02:44:04] Rep: 20 Mol:4 +139: [02:44:04] Rep: 20 Mol:8 +139: [02:44:04] Rep: 20 Mol:12 +139: [02:44:04] Rep: 20 Mol:16 +139: [02:44:04] Rep: 20 Mol:20 +139: [02:44:04] Rep: 20 Mol:24 +139: [02:44:04] Rep: 20 Mol:1 +139: [02:44:04] Rep: 20 Mol:5 +139: [02:44:04] Rep: 20 Mol:9 +139: [02:44:04] Rep: 20 Mol:28 +139: [02:44:04] Rep: 20 Mol:13 +139: [02:44:04] Rep: 20 Mol:17 +139: [02:44:04] Rep: 20 Mol:21 +139: [02:44:04] Rep: 20 Mol:25 +139: [02:44:04] Rep: 20 Mol:29 +145: [02:44:04] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 1 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 1 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 1 +139: [02:44:04] Rep: 40 Mol:3 +139: [02:44:04] Rep: 40 Mol:7 +139: [02:44:04] Rep: 40 Mol:11 +139: [02:44:04] Rep: 40 Mol:15 +139: [02:44:04] Rep: 40 Mol:19 +139: [02:44:04] Rep: 40 Mol:23 +139: [02:44:04] Rep: 40 Mol:27 +139: [02:44:04] Rep: 40 Mol:31 +141: [02:44:04] Rep: 100 Mol:2 +141: [02:44:04] Rep: 100 Mol:6 +141: [02:44:04] Rep: 100 Mol:10 +141: [02:44:04] Rep: 100 Mol:14 +141: [02:44:04] Rep: 100 Mol:18 +141: [02:44:04] Rep: 100 Mol:22 +141: [02:44:04] Rep: 100 Mol:26 +141: [02:44:04] Rep: 100 Mol:30 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 5 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 5 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 5 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 6 +139: [02:44:04] Rep: 40 Mol:0 +139: [02:44:04] Rep: 40 Mol:4 +145: [02:44:04] UFFTYPER: Unrecognized charge state for atom: 6 +139: [02:44:04] Rep: 40 Mol:1 +139: [02:44:04] Rep: 40 Mol:5 +139: [02:44:04] Rep: 40 Mol:9 +139: [02:44:04] Rep: 40 Mol:8 +139: [02:44:04] Rep: 40 Mol:12 +139: [02:44:04] Rep: 40 Mol:16 +139: [02:44:04] Rep: 20 Mol:2 +139: [02:44:04] Rep: 40 Mol:20 +139: [02:44:05] Rep: 40 Mol:13 +139: [02:44:05] Rep: 40 Mol:17 +139: [02:44:05] Rep: 40 Mol:24 +139: [02:44:05] Rep: 40 Mol:21 +139: [02:44:05] Rep: 40 Mol:25 +139: [02:44:05] Rep: 20 Mol:6 +139: [02:44:05] Rep: 20 Mol:10 +139: [02:44:05] Rep: 40 Mol:28 +139: [02:44:05] Rep: 40 Mol:29 +139: [02:44:05] Rep: 20 Mol:14 +139: [02:44:05] Rep: 20 Mol:18 +145: [02:44:05] UFFTYPER: Unrecognized charge state for atom: 6 +139: [02:44:05] Rep: 20 Mol:22 +139: [02:44:05] Rep: 20 Mol:26 +139: [02:44:05] Rep: 20 Mol:30 +141: [02:44:05] Rep: 100 Mol:1 +141: [02:44:05] Rep: 100 Mol:5 +141: [02:44:05] Rep: 100 Mol:9 +141: [02:44:05] Rep: 100 Mol:13 +141: [02:44:05] Rep: 100 Mol:17 +141: [02:44:05] Rep: 100 Mol:21 +141: [02:44:05] Rep: 100 Mol:25 +141: [02:44:05] Rep: 100 Mol:29 +141: [02:44:05] Rep: 100 Mol:0 +141: [02:44:05] Rep: 100 Mol:4 +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +141: [02:44:05] Rep: 100 Mol:8 +141: [02:44:05] Rep: 100 Mol:12 +141: [02:44:05] Rep: 100 Mol:16 +141: [02:44:05] Rep: 100 Mol:20 +141: [02:44:05] Rep: 100 Mol:24 +141: [02:44:05] Rep: 100 Mol:28 +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test unfolded version of RDKFP +126: [02:44:05] ------------------------------------- +126: [02:44:05] Test bitinfo of RDKFP +126: 562: [ 2 ], +126: 709: [ 0 1 ], +126: 1118: [ 0 1 2 ], +126: 1183: [ 1 2 ], +126: 1233: [ 0 1 2 ], +126: 1308: [ 0 ], [ 1 ], +126: 1339: [ 2 ], +126: 1728: [ 1 2 ], +126: 1772: [ 0 ], [ 1 ], +126: 1813: [ 0 1 ], +126: ------------ +126: [02:44:05] ------------------------------------- +126: [02:44:05] Single atoms setting radius 1 bits in Morgan fingerprints +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #879: Pattern fingerprint should set bits for single-atom fragments. +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +115: =>start test GETAWAY custom +115: [02:44:05] test on : 365 molecules done +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +136/230 Test #115: testRDFcustom .......................... Passed 11.53 sec test 146 Start 146: pyDistGeomHelpers 146: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 146: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 146: Test timeout computed to be: 1500 -141: generating reference data -39: [06:21:47] Finished -39: [06:21:47] testing smiles round-tripping. -125/230 Test #143: pyForceFieldHelpers ....................***Exception: SegFault 0.28 sec - +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #2115: BitInfo not complete for RDKFingerprint +126: [02:44:05] done +126: [02:44:05] ------------------------------------- +126: [02:44:05] Github #3723: Fingerprint crash for mols with Zero order bonds +126: [02:44:05] done +137/230 Test #126: testFingerprints ....................... Passed 7.30 sec test 147 Start 147: testMolAlign 147: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 147: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign 147: Test timeout computed to be: 1500 -145: Randomness seeded to: 2185709593 -139: processing -139: launch :0 -139: launch :1 -139: launch :2 -139: launch :3 -139: [06:21:47] Rep: 0 Mol:3 -139: [06:21:47] Rep: 0 Mol:1 -139: [06:21:47] [06:21:47] Rep: 0 Mol:2 -139: Rep: 0 Mol:0 -139: [06:21:47] Rep: 0 Mol:5 -139: [06:21:47] Rep: 0 Mol:9 -145: [06:21:47] [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)] -145: [06:21:47] [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)] -139: [06:21:47] Rep: 0 Mol:4 -145: [06:21:47] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -139: [06:21:47] Rep: 0 Mol:13 -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -139: [06:21:47] Rep: 0 Mol:7 -139: [06:21:47] Rep: 0 Mol:11 -139: [06:21:47] Rep: 0 Mol:15 -145: [06:21:47] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(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)] -139: [06:21:47] Rep: 0 Mol:19 -139: [06:21:47] Rep: 0 Mol:17 -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -139: [06:21:47] Rep: 0 Mol:23 -139: [06:21:47] Rep: 0 Mol:27 -139: [06:21:47] Rep: 0 Mol:6 -139: [06:21:47] Rep: 0 Mol:8 -145: [06:21:47] 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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [!#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)] -145: [06:21:47] [!#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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -139: [06:21:47] Rep: 0 Mol:31 -145: ----------- -139: [06:21:47] Rep: 0 Mol:12 -139: [06:21:47] Rep: 0 Mol:10 -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [$([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)] -145: [06:21:47] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [06:21:47] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -139: [06:21:47] Rep: 0 Mol:16 -145: [06:21:47] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -145: [06:21:47] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -145: ----------- -145: [06:21:47] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$([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)] -145: [06:21:47] [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)] -145: [06:21:47] 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)] -145: ----------- -139: [06:21:47] Rep: 0 Mol:20 -145: ----------- -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -145: [06:21:47] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [06:21:47] [$(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)] -139: [06:21:47] Rep: 0 Mol:24 -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] -145: [06:21:47] [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)] +139: [02:44:05] Rep: 60 Mol:3 +139: [02:44:05] Rep: 60 Mol:7 +139: [02:44:05] Rep: 60 Mol:11 +139: [02:44:05] Rep: 60 Mol:15 +139: [02:44:05] Rep: 60 Mol:19 +139: [02:44:05] Rep: 60 Mol:23 +139: [02:44:05] Rep: 60 Mol:27 +139: [02:44:05] Rep: 60 Mol:31 +139: [02:44:05] Rep: 60 Mol:0 +139: [02:44:05] Rep: 60 Mol:4 +139: [02:44:05] Rep: 60 Mol:8 +139: [02:44:05] Rep: 60 Mol:12 +139: [02:44:05] Rep: 60 Mol:1 +139: [02:44:05] Rep: 60 Mol:5 +139: [02:44:05] Rep: 60 Mol:9 +139: [02:44:05] Rep: 60 Mol:13 +139: [02:44:05] Rep: 60 Mol:16 +139: [02:44:05] Rep: 60 Mol:17 +139: [02:44:05] Rep: 60 Mol:21 +139: [02:44:05] Rep: 60 Mol:25 +139: [02:44:05] Rep: 60 Mol:29 +139: [02:44:05] Rep: 60 Mol:20 +139: [02:44:05] Rep: 60 Mol:24 +139: [02:44:05] Rep: 60 Mol:28 147: *********************************************************** 147: Testing MolAlign 147: --------------------------------- @@ -28020,121 +28574,254 @@ 147: testIssue241 147: 147: *********************************************************** -139: [06:21:47] Rep: 0 Mol:28 -126/230 Test #147: testMolAlign ........................... Passed 0.18 sec +138/230 Test #147: testMolAlign ........................... Passed 0.46 sec test 148 Start 148: testO3AAlign 148: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 148: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign 148: Test timeout computed to be: 1500 -139: [06:21:47] Rep: 0 Mol:21 -139: [06:21:47] Rep: 0 Mol:25 -139: [06:21:47] Rep: 0 Mol:29 -39: [06:21:47] Finished -39: [06:21:47] testing github #1567: Non-canonical result from MolFragmentToSmiles() -39: [06:21:47] Finished -139: [06:21:48] Rep: 0 Mol:14 -127/230 Test #39: hanoiTest .............................. Passed 4.63 sec +139: [02:44:05] Rep: 40 Mol:2 +139: [02:44:05] Rep: 40 Mol:6 +139: [02:44:05] Rep: 40 Mol:10 +139/230 Test #146: pyDistGeomHelpers ......................***Exception: SegFault 0.53 sec + test 149 Start 149: molAlignCatchTest 149: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 149: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -128/230 Test #146: pyDistGeomHelpers ......................***Exception: SegFault 0.34 sec - +139: [02:44:05] Rep: 40 Mol:14 +139: [02:44:05] Rep: 40 Mol:18 +139: [02:44:05] Rep: 40 Mol:22 +139: [02:44:05] Rep: 40 Mol:26 +139: [02:44:05] Rep: 40 Mol:30 +139: [02:44:05] Rep: 80 Mol:3 +139: [02:44:05] Rep: 80 Mol:7 +139: [02:44:05] Rep: 80 Mol:11 +139: [02:44:05] Rep: 80 Mol:15 +139: [02:44:05] Rep: 80 Mol:19 +139: [02:44:05] Rep: 80 Mol:23 +139: [02:44:05] Rep: 80 Mol:27 +139: [02:44:05] Rep: 80 Mol:31 +149: Randomness seeded to: 2194259798 +149: 125797133 +149: 105249814 +139: [02:44:06] Rep: 80 Mol:0 +139: [02:44:06] Rep: 80 Mol:4 +139: [02:44:06] Rep: 80 Mol:1 +139: [02:44:06] Rep: 80 Mol:8 +139: [02:44:06] Rep: 80 Mol:5 +139: [02:44:06] Rep: 80 Mol:9 +139: [02:44:06] Rep: 80 Mol:12 +139: [02:44:06] Rep: 80 Mol:13 +139: [02:44:06] Rep: 80 Mol:17 +139: [02:44:06] Rep: 80 Mol:21 +139: [02:44:06] Rep: 80 Mol:25 +139: [02:44:06] Rep: 80 Mol:29 +139: [02:44:06] Rep: 80 Mol:16 +139: [02:44:06] Rep: 80 Mol:20 +139: [02:44:06] Rep: 80 Mol:24 +139: [02:44:06] Rep: 80 Mol:28 +139: [02:44:06] Rep: 60 Mol:2 +139: [02:44:06] Rep: 60 Mol:6 +139: [02:44:06] Rep: 60 Mol:10 +139: [02:44:06] Rep: 60 Mol:14 +139: [02:44:06] Rep: 60 Mol:18 +139: [02:44:06] Rep: 60 Mol:22 +139: [02:44:06] Rep: 60 Mol:26 +139: [02:44:06] Rep: 60 Mol:30 +141: [02:44:06] done +141: [02:44:06] ------------------------------------- +141: [02:44:06] Test UFF multithreading2 +145: [02:44:06] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +144: [02:44:03] --------------------------------- +144: [02:44:03] test3 +144: +144: [02:44:03] --------------------------------- +144: [02:44:03] test4 +144: +144: [02:44:03] --------------------------------- +144: [02:44:03] test5 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] test6 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] test15Dists +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] test Issue 215 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testMultipleConfs +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testMultipleConfsExpTors +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue227 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue236 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testOrdering +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue244 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue251 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue276 +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue284 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue285 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testIssue355 +144: +144: [02:44:06] --------------------------------- +144: [02:44:06] testRandomCoords +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 1989539 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 2091864 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test constrained embedding +144: +144: [02:44:07] ssd: 0.0752641 +144: [02:44:07] ssd: 0.0659363 +145: [02:44:07] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +145: [02:44:07] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +123: Warning: Atom Count for residue GLU5A does not match expected count +123: Warning: Atom Count for residue ASN39A does not match expected count +123: Warning: Atom Count for residue GLU53A does not match expected count +123: Warning: Atom Count for residue ARG64A does not match expected count +123: Warning: Atom Count for residue LYS80A does not match expected count +123: Warning: Atom Count for residue GLU150A does not match expected count +123: Warning: Atom Count for residue ASN157A does not match expected count +145: [02:44:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +145: [02:44:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +145: [02:44:07] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +123: =============================================================================== +123: All tests passed (515 assertions in 10 test cases) +123: +140/230 Test #123: descriptorsTestCatch ................... Passed 10.32 sec test 150 Start 150: pyMolAlign 150: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 150: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap 150: Test timeout computed to be: 1500 -139: [06:21:48] Rep: 20 Mol:3 -139: [06:21:48] Rep: 20 Mol:7 -139: [06:21:48] Rep: 20 Mol:11 -139: [06:21:48] Rep: 20 Mol:15 -139: [06:21:48] Rep: 20 Mol:19 -139: [06:21:48] Rep: 20 Mol:23 -139: [06:21:48] Rep: 20 Mol:27 -139: [06:21:48] Rep: 20 Mol:31 -139: [06:21:48] Rep: 0 Mol:18 -129/230 Test #41: resMolSupplierTest ..................... Passed 4.65 sec +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 2091974 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 2835784 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 3019283 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 3238580 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test sf.net issue 3483968 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test github issue 55 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test1 +144: +144: [02:44:07] --------------------------------- +144: [02:44:07] test multi-threading +144: +144: building molecules +139: [02:44:07] Rep: 80 Mol:2 +139: [02:44:07] Rep: 80 Mol:6 +139: [02:44:07] Rep: 80 Mol:10 +139: [02:44:07] Rep: 80 Mol:14 +139: [02:44:07] Rep: 80 Mol:18 +139: [02:44:07] Rep: 80 Mol:22 +139: [02:44:07] Rep: 80 Mol:26 +139: [02:44:07] Rep: 80 Mol:30 +144: generating reference data +141: [02:44:08] done +141: [02:44:08] ------------------------------------- +141: [02:44:08] Test UFF multithreading3 +141/230 Test #150: pyMolAlign .............................***Exception: SegFault 0.65 sec + test 151 Start 151: testFeatures 151: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures 151: Test timeout computed to be: 1500 -139: [06:21:48] Rep: 0 Mol:22 -145: [06:21:48] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -115: =>start test rdf custom -115: [06:21:48] test on : 365 molecules done -139: [06:21:48] Rep: 0 Mol:26 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 1 -151: [06:21:48] ------------------------------------- -151: [06:21:48] AtomType parser testing. -151: [06:21:48] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -151: [06:21:48] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] FeatureDefinition parser testing. -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Test pulling feat defs from a string. -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] FeatureDef functionality testing. -139: [06:21:48] Rep: 0 Mol:30 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 1 -139: [06:21:48] Rep: 20 Mol:0 -139: [06:21:48] Rep: 20 Mol:4 -139: [06:21:48] Rep: 20 Mol:8 -139: [06:21:48] Rep: 20 Mol:12 -139: [06:21:48] Rep: 20 Mol:16 -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] FeatureFactory testing. -151: [06:21:48] 1 -151: [06:21:48] 2 -151: [06:21:48] 3 -151: [06:21:48] 4 -151: [06:21:48] 5 -151: [06:21:48] 6 -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Feature Location testing. -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Test building a FeatureFactory from a file -139: [06:21:48] Rep: 20 Mol:20 -139: [06:21:48] Rep: 20 Mol:24 -139: [06:21:48] Rep: 20 Mol:28 -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing Issue 224. -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing Issue 225. -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Test Issue346 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 1 -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Test Issue347 -151: [06:21:48] done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing Issue 348. -151: [06:21:48] SMARTS Parse Error: syntax error while parsing: [C[C] -151: [06:21:48] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing Nested AtomType definitions. +139: [02:44:08] done +139: [02:44:08] ------------------------------------- +139: [02:44:08] Test MMFF multithreading2 +151: [02:44:08] ------------------------------------- +151: [02:44:08] AtomType parser testing. +151: [02:44:08] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +151: [02:44:08] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] FeatureDefinition parser testing. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Test pulling feat defs from a string. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] FeatureDef functionality testing. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] FeatureFactory testing. +151: [02:44:08] 1 +151: [02:44:08] 2 +151: [02:44:08] 3 +151: [02:44:08] 4 +151: [02:44:08] 5 +151: [02:44:08] 6 +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Feature Location testing. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Test building a FeatureFactory from a file +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing Issue 224. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing Issue 225. +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Test Issue346 +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Test Issue347 +151: [02:44:08] done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing Issue 348. +151: [02:44:08] SMARTS Parse Error: syntax error while parsing: [C[C] +151: [02:44:08] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing Nested AtomType definitions. 151: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing Github Issue #252: crash when calling getPos() with no conformer. -151: [06:21:48] expect a precondition failure message below -151: [06:21:48] +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing Github Issue #252: crash when calling getPos() with no conformer. +151: [02:44:08] expect a precondition failure message below +151: [02:44:08] 151: 151: **** 151: Pre-condition Violation @@ -28147,82 +28834,33 @@ 151: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 151: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 151: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -151: 4# 0x5658D0F3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 5# 0x5658049D in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 6# 0xF766DD43 in /lib/i386-linux-gnu/libc.so.6 +151: 4# 0x566500F3 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 5# 0x5664349D in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 6# 0xF76BED43 in /lib/i386-linux-gnu/libc.so.6 151: 7# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -151: 8# 0x565805A7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 8# 0x566435A7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: ---------- 151: **** 151: -151: [06:21:48] Done -151: [06:21:48] ------------------------------------- -151: [06:21:48] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -151: [06:21:48] done -130/230 Test #151: testFeatures ........................... Passed 0.09 sec +151: [02:44:08] Done +151: [02:44:08] ------------------------------------- +151: [02:44:08] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +151: [02:44:08] done +142/230 Test #151: testFeatures ........................... Passed 0.10 sec test 152 Start 152: pyChemicalFeatures 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 152: Test timeout computed to be: 1500 -149: Randomness seeded to: 35020737 -149: 85740920 -139: [06:21:48] Rep: 40 Mol:3 -139: [06:21:48] Rep: 40 Mol:7 -139: [06:21:48] Rep: 40 Mol:11 -139: [06:21:48] Rep: 40 Mol:15 -139: [06:21:48] Rep: 40 Mol:19 -139: [06:21:48] Rep: 40 Mol:23 -139: [06:21:48] Rep: 40 Mol:27 -139: [06:21:48] Rep: 40 Mol:31 -141: processing -141: launch :0 -141: launch :1 -141: [06:21:48] Rep: 0 Mol:0 -141: launch :2 -141: launch :3 -141: [06:21:48] Rep: 0 Mol:2 -141: [06:21:48] Rep: 0 Mol:1 -141: [06:21:48] Rep: 0 Mol:3 -141: [06:21:48] Rep: 0 Mol:5 -141: [06:21:48] Rep: 0 Mol:4 -139: [06:21:48] Rep: 20 Mol:1 -139: [06:21:48] Rep: 20 Mol:5 -139: [06:21:48] Rep: 20 Mol:9 -139: [06:21:48] Rep: 20 Mol:13 -139: [06:21:48] Rep: 20 Mol:17 -139: [06:21:48] Rep: 20 Mol:21 -139: [06:21:48] Rep: 20 Mol:25 -141: [06:21:48] Rep: 0 Mol:9 -139: [06:21:48] Rep: 20 Mol:29 -120: =>start test GETAWAY -120: [06:21:48] test on : 365 molecules done -149: 61479027 -131/230 Test #120: testGETAWAY ............................ Passed 2.82 sec +143/230 Test #152: pyChemicalFeatures .....................***Exception: SegFault 1.33 sec + test 153 Start 153: testShapeHelpers 153: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 153: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers 153: Test timeout computed to be: 1500 -141: [06:21:48] Rep: 0 Mol:6 -141: [06:21:48] Rep: 0 Mol:8 -141: [06:21:48] Rep: 0 Mol:7 -141: [06:21:48] Rep: 0 Mol:11 -141: [06:21:48] Rep: 0 Mol:13 -141: [06:21:48] Rep: 0 Mol:10 -141: [06:21:48] Rep: 0 Mol:12 -141: [06:21:48] Rep: 0 Mol:16 -141: [06:21:48] Rep: 0 Mol:15 -141: [06:21:48] Rep: 0 Mol:19 -141: [06:21:48] Rep: 0 Mol:20 -141: [06:21:48] Rep: 0 Mol:17 -141: [06:21:48] Rep: 0 Mol:24 -141: [06:21:48] Rep: 0 Mol:23 -141: [06:21:48] Rep: 0 Mol:27 -141: [06:21:48] Rep: 0 Mol:28 -141: [06:21:48] Rep: 0 Mol:31 153: *********************************************************** 153: Testing ShapeHelpers 153: --------------------------------- @@ -28235,61 +28873,14 @@ 153: testGithub4364 153: 153: *********************************************************** -132/230 Test #153: testShapeHelpers ....................... Passed 0.07 sec +144/230 Test #153: testShapeHelpers ....................... Passed 0.21 sec test 154 Start 154: pyShapeHelpers 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 154: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 154: Test timeout computed to be: 1500 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 5 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 5 -123: Warning: Atom Count for residue GLU150A does not match expected count -141: [06:21:48] Rep: 0 Mol:14 -141: [06:21:48] Rep: 0 Mol:21 -141: [06:21:48] Rep: 0 Mol:18 -141: [06:21:48] Rep: 0 Mol:25 -141: [06:21:48] Rep: 0 Mol:22 -139: [06:21:48] Rep: 40 Mol:0 -139: [06:21:48] Rep: 40 Mol:4 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 5 -141: [06:21:48] Rep: 0 Mol:26 -139: [06:21:48] Rep: 40 Mol:8 -139: [06:21:48] Rep: 40 Mol:12 -139: [06:21:48] Rep: 40 Mol:16 -139: [06:21:48] Rep: 40 Mol:20 -139: [06:21:48] Rep: 40 Mol:24 -139: [06:21:48] Rep: 40 Mol:28 -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test Issue252: Bad definitions for Crippen atom types. -141: [06:21:48] Rep: 0 Mol:30 -141: [06:21:48] Rep: 0 Mol:29 -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of ChiVs. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of ChiNs. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of HallKierAlpha. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of Kappa1. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of Kappa2. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of Kappa3. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test Crippen atom type calculations. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test ring descriptors -133/230 Test #150: pyMolAlign .............................***Exception: SegFault 0.38 sec +145/230 Test #154: pyShapeHelpers .........................***Exception: SegFault 0.54 sec test 155 Start 155: testMolCatalog @@ -28297,222 +28888,54 @@ 155: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 155: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolCatalog 155: Test timeout computed to be: 1500 -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test other count descriptors. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test MQN -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test GitHub Issue 56. -109: [06:21:48] WARNING: not removing hydrogen atom without neighbors -109: [06:21:48] WARNING: not removing hydrogen atom without neighbors -109: [06:21:48] WARNING: not removing hydrogen atom without neighbors -109: [06:21:48] WARNING: not removing hydrogen atom without neighbors -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test Github92: Bad Crippen atom type for pyrrole H. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test Github362: order dependence in Kier-Hall descriptors. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test calculation of spiro and bridgehead counts. -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Test Github694: ExactMolWt ignoring the mass of the electron -109: [06:21:48] done -109: [06:21:48] ------------------------------------- -109: [06:21:48] Testing Properties and KitchenSink -109: [06:21:48] ---Caught keyerror (bad property name)--- -109: [06:21:48] -109: -109: **** -109: Test Assert -109: Expression Failed: -109: Violation occurred on line 1971 in file ./Code/GraphMol/Descriptors/test.cpp -109: Failed Expression: pq->Match(*mol) -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x5663F417 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -109: 3# 0x566375F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -109: 4# 0xF7416D43 in /lib/i386-linux-gnu/libc.so.6 -109: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -109: 6# 0x56637AD7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -109: ---------- -109: **** -109: -109: terminate called after throwing an instance of 'Invar::Invariant' -109: what(): Expression Failed: -134/230 Test #109: testDescriptors ........................Subprocess aborted***Exception: 3.66 sec -[06:21:44] ------------------------------------- -[06:21:44] Test Crippen parameter acquisition. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test Crippen calculation. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test Issue262: problems with Crippen calculation from pickles. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test AMW calculation. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test Exact MW calculation. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test Labute ASA descriptors. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test TPSA descriptors. -[06:21:44] done -[06:21:44] ------------------------------------- -[06:21:44] Test Lipinski parameters. -[06:21:45] done -[06:21:45] ------------------------------------- -[06:21:45] Test VSA descriptors. -[06:21:45] done -[06:21:45] ------------------------------------- -[06:21:45] Test molecular formula calculation. -[06:21:45] done -[06:21:45] ------------------------------------- -[06:21:45] Test Issue 3415534. -[06:21:45] done -[06:21:45] ------------------------------------- -[06:21:45] Test Issue3433771: Bad definition for Crippen atom type O11. -[06:21:45] done -[06:21:45] ------------------------------------- -[06:21:45] Test multithreading -reading molecules -processing - launch :0 - launch :1 - launch :2 - launch :3 -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test Issue252: Bad definitions for Crippen atom types. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of ChiVs. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of ChiNs. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of HallKierAlpha. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of Kappa1. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of Kappa2. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of Kappa3. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test Crippen atom type calculations. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test ring descriptors -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test other count descriptors. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test MQN -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test GitHub Issue 56. -[06:21:48] WARNING: not removing hydrogen atom without neighbors -[06:21:48] WARNING: not removing hydrogen atom without neighbors -[06:21:48] WARNING: not removing hydrogen atom without neighbors -[06:21:48] WARNING: not removing hydrogen atom without neighbors -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test Github92: Bad Crippen atom type for pyrrole H. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test Github362: order dependence in Kier-Hall descriptors. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test calculation of spiro and bridgehead counts. -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Test Github694: ExactMolWt ignoring the mass of the electron -[06:21:48] done -[06:21:48] ------------------------------------- -[06:21:48] Testing Properties and KitchenSink -[06:21:48] ---Caught keyerror (bad property name)--- -[06:21:48] - -**** -Test Assert -Expression Failed: -Violation occurred on line 1971 in file ./Code/GraphMol/Descriptors/test.cpp -Failed Expression: pq->Match(*mol) ----------- -Stacktrace: - 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 2# 0x5663F417 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors - 3# 0x566375F2 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors - 4# 0xF7416D43 in /lib/i386-linux-gnu/libc.so.6 - 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 - 6# 0x56637AD7 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors ----------- -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - +146/230 Test #155: testMolCatalog ......................... Passed 0.07 sec test 156 Start 156: pyMolCatalog 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 156: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap 156: Test timeout computed to be: 1500 -139: [06:21:48] Rep: 60 Mol:3 -139: [06:21:48] Rep: 60 Mol:7 -139: [06:21:48] Rep: 60 Mol:11 -139: [06:21:48] Rep: 60 Mol:15 -139: [06:21:48] Rep: 60 Mol:19 -139: [06:21:48] Rep: 60 Mol:23 -139: [06:21:48] Rep: 60 Mol:27 -139: [06:21:48] Rep: 60 Mol:31 -135/230 Test #155: testMolCatalog ......................... Passed 0.03 sec +141: [02:44:10] done +141: [02:44:10] ------------------------------------- +141: [02:44:10] Testing GitHubIssue62. +141: [02:44:10] beta-lactam 39.6387 +141: [02:44:10] cyclopropanone 174.698 +141: [02:44:10] aziridine 337.986 +141: [02:44:10] aziridinone 115.248 +141: [02:44:10] isobutene 2.48217 +141: [02:44:10] acetone 1.91788 +141: [02:44:10] cyclopentanone 10.1648 +141: [02:44:10] cyclopropene 99.4921 +141: [02:44:10] cyclobutene 41.0156 +141: [02:44:10] cyclopropane 267.236 +141: [02:44:10] gamma-lactam 15.7471 +141: [02:44:10] trans-2,3-diphenylcyclopropan-1-one 203.398 +141: [02:44:10] cis-2,3-diphenylcyclopropan-1-one 206.852 +139: [02:44:10] done +139: [02:44:10] ------------------------------------- +139: [02:44:10] Test MMFF multithreading3 +141: [02:44:10] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +141: [02:44:10] cyclopropylidencyclobutane 218.879 +147/230 Test #156: pyMolCatalog ...........................***Exception: SegFault 0.36 sec + test 157 Start 157: moldraw2DTest1 157: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 157: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 157: Test timeout computed to be: 1500 -139: [06:21:48] Rep: 20 Mol:2 -139: [06:21:48] Rep: 20 Mol:6 -139: [06:21:48] Rep: 20 Mol:10 -139: [06:21:48] Rep: 20 Mol:14 -123: Warning: Atom Count for residue ASN157A does not match expected count -139: [06:21:48] Rep: 20 Mol:18 -139: [06:21:48] Rep: 20 Mol:22 -139: [06:21:48] Rep: 20 Mol:26 -139: [06:21:48] Rep: 20 Mol:30 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 6 -139: [06:21:48] Rep: 40 Mol:1 -139: [06:21:48] Rep: 40 Mol:5 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 6 -139: [06:21:48] Rep: 40 Mol:9 -139: [06:21:48] Rep: 40 Mol:13 -139: [06:21:48] Rep: 40 Mol:17 -139: [06:21:48] Rep: 40 Mol:21 -139: [06:21:48] Rep: 40 Mol:25 -139: [06:21:48] Rep: 40 Mol:29 -145: [06:21:48] UFFTYPER: Unrecognized charge state for atom: 6 -136/230 Test #152: pyChemicalFeatures .....................***Exception: SegFault 0.39 sec - +141: [02:44:11] diphenylmethylidencyclobutane 79.6139 +141: [02:44:11] done +141: [02:44:11] ------------------------------------- +141: [02:44:11] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +141: [02:44:11] done +141: [02:44:11] ------------------------------------- +141: [02:44:11] Test square planar complexes +141: [02:44:11] done +141: [02:44:11] ------------------------------------- +141: [02:44:11] Test octahedral complexes +141: [02:44:11] done +148/230 Test #141: testUFFForceFieldHelpers ............... Passed 9.45 sec test 158 Start 158: moldraw2DTestCatch @@ -28524,14 +28947,14 @@ 157: file test1_2.svg gave hash 2870923971U not the expected 1799670018U 157: file test1_3.svg gave hash 4061311478U not the expected 2382509631U 157: file test1_4.svg gave hash 2391498639U not the expected 4252277495U +158: Randomness seeded to: 1752506135 +158: file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U 157: file test1_5.svg gave hash 3746760138U not the expected 2811480876U 157: file test1_6.svg gave hash 3385405097U not the expected 2635907956U +158: file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U 157: file test1_7.svg gave hash 996285542U not the expected 3677608850U 157: Done 157: ----------------- Test 2 -158: Randomness seeded to: 3036021413 -158: file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U -158: file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U 158: file testAtomTags_3.svg gave hash 4222259109U not the expected 2244078420U 157: file test2_1.png gave hash 1061714059U not the expected 307437906U 157: file test2_2.png gave hash 4033022735U not the expected 610424244U @@ -28543,32 +28966,14 @@ 157: ----------------- Test 5 157: file test5_1.png gave hash 3809833703U not the expected 1269428339U 157: file test5_1.svg gave hash 1599298648U not the expected 4074479420U -139: [06:21:48] Rep: 60 Mol:0 -139: [06:21:48] Rep: 60 Mol:4 -139: [06:21:48] Rep: 60 Mol:8 -139: [06:21:48] Rep: 60 Mol:12 157: file test5_2.png gave hash 864977839U not the expected 3073694291U 157: file test5_2.svg gave hash 3060847100U not the expected 1125439478U -139: [06:21:48] Rep: 60 Mol:16 -139: [06:21:48] Rep: 60 Mol:20 -139: [06:21:48] Rep: 60 Mol:24 -158: file contourMol_1.svg gave hash 929279459U not the expected 2604538953U -139: [06:21:48] Rep: 80 Mol:3 -139: [06:21:48] Rep: 80 Mol:7 157: file test5_3.png gave hash 974088371U not the expected 1865192682U 157: file test5_3.svg gave hash 78536282U not the expected 3322548698U 157: Done 157: ----------------- Test 6 (atom labels) -139: [06:21:48] Rep: 80 Mol:11 -139: [06:21:48] Rep: 60 Mol:28 -139: [06:21:48] Rep: 80 Mol:15 -139: [06:21:48] Rep: 80 Mol:19 -139: [06:21:48] Rep: 80 Mol:23 -139: [06:21:48] Rep: 80 Mol:27 -139: [06:21:48] Rep: 80 Mol:31 157: file test6_1.svg gave hash 893244114U not the expected 3623418420U -158: file contourMol_2.svg gave hash 783162854U not the expected 572669511U -157: [06:21:48] +157: [02:44:11] 157: 157: **** 157: Test Assert @@ -28579,17 +28984,17 @@ 157: Stacktrace: 157: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 157: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 -157: 2# 0x565D29A8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 -157: 3# 0x565C1279 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 -157: 4# 0xF713AD43 in /lib/i386-linux-gnu/libc.so.6 +157: 2# 0x5658D9A8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 +157: 3# 0x5657C279 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 +157: 4# 0xF71A6D43 in /lib/i386-linux-gnu/libc.so.6 157: 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -157: 6# 0x565C1397 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 +157: 6# 0x5657C397 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 157: ---------- 157: **** 157: 157: terminate called after throwing an instance of 'Invar::Invariant' 157: what(): Expression Failed: -137/230 Test #157: moldraw2DTest1 .........................Subprocess aborted***Exception: 0.27 sec +149/230 Test #157: moldraw2DTest1 .........................Subprocess aborted***Exception: 0.51 sec ----------------- Test 1 file test1_1.svg gave hash 2024041829U not the expected 1617157703U file test1_2.svg gave hash 2870923971U not the expected 1799670018U @@ -28617,7 +29022,7 @@ Done ----------------- Test 6 (atom labels) file test6_1.svg gave hash 893244114U not the expected 3623418420U -[06:21:48] +[02:44:11] **** Test Assert @@ -28628,11 +29033,11 @@ Stacktrace: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitRDGeneral.so.1 - 2# 0x565D29A8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 - 3# 0x565C1279 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 - 4# 0xF713AD43 in /lib/i386-linux-gnu/libc.so.6 + 2# 0x5658D9A8 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 + 3# 0x5657C279 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 + 4# 0xF71A6D43 in /lib/i386-linux-gnu/libc.so.6 5# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 - 6# 0x565C1397 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 + 6# 0x5657C397 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 ---------- **** @@ -28645,25 +29050,15 @@ 159: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 +149: 5379424805 +158: file contourMol_1.svg gave hash 929279459U not the expected 2604538953U +158: file contourMol_2.svg gave hash 783162854U not the expected 572669511U +159: ----------------- Test 1 158: file contourMol_3.svg gave hash 2555433126U not the expected 936771429U 158: file contourMol_4.svg gave hash 975463245U not the expected 3302971362U -138/230 Test #156: pyMolCatalog ...........................***Exception: SegFault 0.31 sec - -test 160 - Start 160: pyMolDraw2D - -160: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -160: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -160: Test timeout computed to be: 1500 -139/230 Test #154: pyShapeHelpers .........................***Exception: SegFault 0.43 sec - -test 161 - Start 161: testFMCS - -161: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/testFMCS -161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS -161: Test timeout computed to be: 1500 +159: file rxn_test1_1.png gave hash 4141159742U not the expected 1556334749U 158: file contourMol_5.svg gave hash 1850401810U not the expected 2230414999U +159: file rxn_test1_1.svg gave hash 3704046125U not the expected 2645695747U 158: file testDativeBonds_1.svg gave hash 280593396U not the expected 3550231997U 158: 158: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28768,46 +29163,21 @@ 158: file testAtomBondIndices_4.svg gave hash 50550161U not the expected 1200363593U 158: file testAtomBondIndices_5.svg gave hash 588466320U not the expected 1502163147U 158: file testAtomBondIndices_6.svg gave hash 2515921087U not the expected 1659568104U +159: file rxn_test1_2.png gave hash 2525477991U not the expected 1924084263U 158: file testGithub3226_1.svg gave hash 2607334889U not the expected 831257877U -159: ----------------- Test 1 +159: file rxn_test1_2.svg gave hash 785569968U not the expected 2640646320U +159: file rxn_test1_3.png gave hash 226541141U not the expected 1644921059U +159: file rxn_test1_3.svg gave hash 1629902707U not the expected 2781928588U 158: file testGithub3226_1.png gave hash 2537777830U not the expected 2350054896U -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 5.293s -12: -12: OK 158: file testGithub3226_2.svg gave hash 2826543129U not the expected 3517325227U 158: file testGithub3226_2.png gave hash 3053251470U not the expected 606206725U 158: file testGithub3226_3.svg gave hash 1034335497U not the expected 3609721552U -140/230 Test #12: pyBV ................................... Passed 5.55 sec -test 162 - Start 162: pyFMCS - -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/testFMCS.py" -162: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap -162: Test timeout computed to be: 1500 158: file testGithub3226_3.png gave hash 3268252519U not the expected 2282880418U +159: file rxn_test1_4.png gave hash 1047103464U not the expected 2471435686U 158: file testPNGMetadata_1.png gave hash 2281415518U not the expected 2423299691U -159: file rxn_test1_1.png gave hash 4141159742U not the expected 1556334749U -159: file rxn_test1_1.svg gave hash 3704046125U not the expected 2645695747U -159: file rxn_test1_2.png gave hash 2525477991U not the expected 1924084263U +159: file rxn_test1_5.png gave hash 1692946948U not the expected 1428782307U +159: file rxn_test1_5.svg gave hash 935208505U not the expected 2762972460U 158: file testPNGMetadata_2.png gave hash 4208175474U not the expected 2803353117U -159: file rxn_test1_2.svg gave hash 785569968U not the expected 2640646320U -139: [06:21:48] Rep: 60 Mol:1 -139: [06:21:48] Rep: 60 Mol:5 -139: [06:21:48] Rep: 60 Mol:9 -139: [06:21:48] Rep: 60 Mol:13 -139: [06:21:48] Rep: 60 Mol:17 -139: [06:21:48] Rep: 60 Mol:21 -139: [06:21:48] Rep: 40 Mol:2 -159: file rxn_test1_3.png gave hash 226541141U not the expected 1644921059U -139: [06:21:48] Rep: 40 Mol:6 -139: [06:21:48] Rep: 40 Mol:10 -139: [06:21:48] Rep: 60 Mol:25 -139: [06:21:48] Rep: 60 Mol:29 -159: file rxn_test1_3.svg gave hash 1629902707U not the expected 2781928588U -139: [06:21:48] Rep: 40 Mol:14 -139: [06:21:48] Rep: 40 Mol:18 158: file testGithub3369_1.svg gave hash 847012018U not the expected 2194263901U 158: file testIncludeRadicals_1a.svg gave hash 491547145U not the expected 1829641340U 158: file testIncludeRadicals_1b.svg gave hash 313150698U not the expected 4184066907U @@ -28833,31 +29203,101 @@ 158: != 158: 4294967295 (0xffffffff) 158: -159: file rxn_test1_4.png gave hash 1047103464U not the expected 2471435686U -139: [06:21:48] Rep: 40 Mol:22 -139: [06:21:48] Rep: 40 Mol:26 -139: [06:21:48] Rep: 40 Mol:30 158: file testGithub3577-1.svg gave hash 1113173858U not the expected 1294276543U -139: [06:21:49] Rep: 80 Mol:0 -139: [06:21:49] Rep: 80 Mol:4 -139: [06:21:49] Rep: 80 Mol:8 -139: [06:21:49] Rep: 80 Mol:12 -139: [06:21:49] Rep: 80 Mol:16 -139: [06:21:49] Rep: 80 Mol:20 -139: [06:21:49] Rep: 80 Mol:24 -159: file rxn_test1_5.png gave hash 1692946948U not the expected 1428782307U -139: [06:21:49] Rep: 80 Mol:28 -115: =>start test morse custom -115: [06:21:49] test on : 365 molecules done -159: file rxn_test1_5.svg gave hash 935208505U not the expected 2762972460U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test1_6.png gave hash 1277214321U not the expected 483353696U 159: file rxn_test1_6.svg gave hash 3859424573U not the expected 2941728011U -141/230 Test #160: pyMolDraw2D ............................***Exception: SegFault 0.32 sec +159: file rxn_test1_7.png gave hash 2451532346U not the expected 528963379U +159: file rxn_test1_7.svg gave hash 742962872U not the expected 1389845691U +159: Done +159: ----------------- Test 2: some examples that caused problems in testing +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-1.png gave hash 2627351917U not the expected 698316547U +159: file rxn_test2_1.png gave hash 2688087453U not the expected 399415052U +159: file rxn_test2_1.svg gave hash 1506865022U not the expected 3791815067U +159: 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 +159: file rxn_test2_2_1.png gave hash 1507801353U not the expected 1215378243U +159: file rxn_test2_2_1.svg gave hash 1799184287U not the expected 2068242269U +159: 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 +159: file rxn_test2_2_2.png gave hash 3350736922U not the expected 3645141778U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test2_2_2.svg gave hash 328158699U not the expected 269990608U +159: 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 +159: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl +159: 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 +159: file rxn_test2_2_3.png gave hash 1857357884U not the expected 551946805U +158: file testHandDrawn-2.svg gave hash 96083296U not the expected 4132716144U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test2_2_3.svg gave hash 2991177755U not the expected 1544919807U +159: 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 +158: file testHandDrawn-2.png gave hash 4101580717U not the expected 1605553248U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test2_2_4.png gave hash 4003629119U not the expected 4234617566U +158: file testHandDrawn-3.svg gave hash 1092525158U not the expected 4199337510U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test2_2_4.svg gave hash 1479905333U not the expected 2015871327U +159: Done +159: ----------------- Test 3: test reactant highlighting +158: file testHandDrawn-3.png gave hash 2781539807U not the expected 2881952238U +139: [02:44:12] done +139: [02:44:12] ------------------------------------- +139: [02:44:12] Testing github 162: Incorrect SMILES after MMFF parameterization . +139: [02:44:12] done +139: [02:44:12] ------------------------------------- +139: [02:44:12] Testing github 224: crash during MMFF parameterization . +139: [02:44:12] done +139: [02:44:12] ------------------------------------- +139: [02:44:12] Testing github6728: crash due to missing stretch-bend params. +150/230 Test #139: testMMFFForceFieldHelpers .............. Passed 11.57 sec +test 160 + Start 160: pyMolDraw2D + +160: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +160: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +160: Test timeout computed to be: 1500 +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-4.svg gave hash 943966498U not the expected 4197407865U +158: [02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test3_1.png gave hash 2195097020U not the expected 4176857511U +158: file testHandDrawn-4.png gave hash 1299432584U not the expected 3431655453U +159: file rxn_test3_1.svg gave hash 1431039304U not the expected 1359061920U +159: Done +159: ----------------- Test 4: some examples from SMARTS in testing +159: draw! +159: file rxn_test4_1.png gave hash 3942497090U not the expected 4187207676U +159: file rxn_test4_1.svg gave hash 3996630280U not the expected 1727161552U +159: done +159: file rxn_test4_2.png gave hash 1540116253U not the expected 3490081297U +159: file rxn_test4_2.svg gave hash 3240313871U not the expected 2032588691U +159: Done +151/230 Test #159: moldraw2DRxnTest1 ...................... Passed 1.76 sec +test 161 + Start 161: testFMCS + +161: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/testFMCS +161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS +161: Test timeout computed to be: 1500 +149: 1688331190 +149: =============================================================================== +149: All tests passed (73 assertions in 3 test cases) +149: +152/230 Test #149: molAlignCatchTest ...................... Passed 7.56 sec +test 162 + Start 162: pyFMCS + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/testFMCS.py" +162: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap +162: Test timeout computed to be: 1500 +153/230 Test #160: pyMolDraw2D ............................***Exception: SegFault 0.41 sec test 163 Start 163: FMCStest @@ -28865,17 +29305,6 @@ 163: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 163: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test 163: Test timeout computed to be: 1500 -116: =>start test rdf -116: [06:21:49] test on : 365 molecules done -158: file testHandDrawn-1.png gave hash 2627351917U not the expected 698316547U -142/230 Test #116: testRDF ................................ Passed 4.04 sec -test 164 - Start 164: molHashCatchTest - -164: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest -164: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash -164: Test timeout computed to be: 1500 -159: file rxn_test1_7.png gave hash 2451532346U not the expected 528963379U 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory @@ -30575,9 +31004,6 @@ 163: 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 163: -159: file rxn_test1_7.svg gave hash 742962872U not the expected 1389845691U -159: Done -159: ----------------- Test 2: some examples that caused problems in testing 163: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory 163: fopen testChEMBL_Txt(): No such file or directory @@ -30844,35 +31270,25 @@ 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 163: ERROR: RDKit could not load input file -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-2.svg gave hash 96083296U not the expected 4132716144U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: file rxn_test2_1.png gave hash 2688087453U not the expected 399415052U -143/230 Test #163: FMCStest ............................... Passed 0.10 sec +154/230 Test #163: FMCStest ............................... Passed 0.04 sec +test 164 + Start 164: molHashCatchTest + +164: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest +164: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash +164: Test timeout computed to be: 1500 +164: Randomness seeded to: 685899881 +164: =============================================================================== +164: All tests passed (332 assertions in 13 test cases) +164: +155/230 Test #164: molHashCatchTest ....................... Passed 0.13 sec test 165 Start 165: pyMolHash 165: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap/testMolHash.py" 165: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap 165: Test timeout computed to be: 1500 -158: file testHandDrawn-2.png gave hash 4101580717U not the expected 1605553248U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-3.svg gave hash 1092525158U not the expected 4199337510U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: file rxn_test2_1.svg gave hash 1506865022U not the expected 3791815067U -159: 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 -158: file testHandDrawn-3.png gave hash 2781539807U not the expected 2881952238U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-4.svg gave hash 943966498U not the expected 4197407865U -158: [06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: file rxn_test2_2_1.png gave hash 1507801353U not the expected 1215378243U -144/230 Test #162: pyFMCS .................................***Exception: SegFault 0.37 sec +156/230 Test #162: pyFMCS .................................***Exception: SegFault 0.45 sec test 166 Start 166: testMMPA @@ -30880,59 +31296,9 @@ 166: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/testMMPA 166: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA 166: Test timeout computed to be: 1500 -158: file testHandDrawn-4.png gave hash 1299432584U not the expected 3431655453U -141: [06:21:49] Rep: 100 Mol:3 -141: [06:21:49] Rep: 100 Mol:7 -141: [06:21:49] Rep: 100 Mol:11 -141: [06:21:49] Rep: 100 Mol:15 -141: [06:21:49] Rep: 100 Mol:19 -141: [06:21:49] Rep: 100 Mol:23 -141: [06:21:49] Rep: 100 Mol:27 -141: [06:21:49] Rep: 100 Mol:31 -159: file rxn_test2_2_1.svg gave hash 1799184287U not the expected 2068242269U -159: 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 -139: [06:21:49] Rep: 60 Mol:2 -139: [06:21:49] Rep: 60 Mol:6 -139: [06:21:49] Rep: 60 Mol:10 -139: [06:21:49] Rep: 60 Mol:14 -139: [06:21:49] Rep: 60 Mol:18 -139: [06:21:49] Rep: 60 Mol:22 -139: [06:21:49] Rep: 60 Mol:26 -159: file rxn_test2_2_2.png gave hash 3350736922U not the expected 3645141778U -139: [06:21:49] Rep: 80 Mol:1 -139: [06:21:49] Rep: 60 Mol:30 -139: [06:21:49] Rep: 80 Mol:5 -159: file rxn_test2_2_2.svg gave hash 328158699U not the expected 269990608U -159: 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 -159: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl -159: 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 -139: [06:21:49] Rep: 80 Mol:9 -139: [06:21:49] Rep: 80 Mol:13 -139: [06:21:49] Rep: 80 Mol:17 -139: [06:21:49] Rep: 80 Mol:21 -159: file rxn_test2_2_3.png gave hash 1857357884U not the expected 551946805U -139: [06:21:49] Rep: 80 Mol:25 -139: [06:21:49] Rep: 80 Mol:29 -159: file rxn_test2_2_3.svg gave hash 2991177755U not the expected 1544919807U -159: 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 -164: Randomness seeded to: 450380163 -164: =============================================================================== -164: All tests passed (332 assertions in 13 test cases) -164: -145/230 Test #164: molHashCatchTest ....................... Passed 0.20 sec -test 167 - Start 167: pyMMPA - -167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/testMMPA.py" -167: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap -167: Test timeout computed to be: 1500 -159: file rxn_test2_2_4.png gave hash 4003629119U not the expected 4234617566U -159: file rxn_test2_2_4.svg gave hash 1479905333U not the expected 2015871327U -159: Done -159: ----------------- Test 3: test reactant highlighting 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.025617 seconds +166: Time elapsed 0.010521 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -30947,7 +31313,6 @@ 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case. -159: file rxn_test3_1.png gave hash 2195097020U not the expected 4176857511U 166: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] @@ -30964,21 +31329,25 @@ 166: 14: NOREF. Reference data NOT LISTED in test case. 166: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 166: 15: NOREF. Reference data NOT LISTED in test case. -159: file rxn_test3_1.svg gave hash 1431039304U not the expected 1359061920U -159: Done -159: ----------------- Test 4: some examples from SMARTS in testing -159: draw! 166: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. 166: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 17: NOREF. Reference data NOT LISTED in test case. 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. +157/230 Test #165: pyMolHash ..............................***Exception: SegFault 0.35 sec + +test 167 + Start 167: pyMMPA + +167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/testMMPA.py" +167: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap +167: Test timeout computed to be: 1500 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 166: ----------------------------------- -166: Time elapsed 0.005565 seconds +166: Time elapsed 0.008503 seconds 166: 166: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 166: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -31011,14 +31380,6 @@ 166: 14: PASSED. matchedRefRes = 11 166: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 15: PASSED. matchedRefRes = 2 -141: [06:21:49] Rep: 100 Mol:2 -141: [06:21:49] Rep: 100 Mol:6 -141: [06:21:49] Rep: 100 Mol:10 -141: [06:21:49] Rep: 100 Mol:14 -141: [06:21:49] Rep: 100 Mol:18 -141: [06:21:49] Rep: 100 Mol:22 -141: [06:21:49] Rep: 100 Mol:26 -141: [06:21:49] Rep: 100 Mol:30 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -31028,7 +31389,7 @@ 166: ----------------------------------- 166: 166: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -166: Time elapsed 0.005424 seconds +166: Time elapsed 0.008274 seconds 166: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 166: 1: PASSED. matchedRefRes = 4 166: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -31047,6 +31408,7 @@ 166: 8: NOREF. Reference data NOT LISTED in test case. 166: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 9: NOREF. Reference data NOT LISTED in test case. +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 166: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 166: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -31055,7 +31417,6 @@ 166: 12: PASSED. matchedRefRes = 8 166: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 13: PASSED. matchedRefRes = 9 -159: file rxn_test4_1.png gave hash 3942497090U not the expected 4187207676U 166: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 14: PASSED. matchedRefRes = 11 166: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] @@ -31069,7 +31430,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -166: Time elapsed 0.001445 seconds +166: Time elapsed 0.003361 seconds 166: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 166: 1: PASSED. matchedRefRes = 2 166: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -31084,8 +31445,6 @@ 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 166: 7: PASSED. matchedRefRes = 7 -159: file rxn_test4_1.svg gave hash 3996630280U not the expected 1727161552U -159: done 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -31093,7 +31452,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.006610 seconds +166: Time elapsed 0.009548 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -31136,7 +31495,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -166: Time elapsed 0.006637 seconds +166: Time elapsed 0.007924 seconds 166: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -31177,32 +31536,14 @@ 166: --- ALL PASSED --- 166: ----------------------------------- 166: 5 TEST CASES FAILED -146/230 Test #166: testMMPA ............................... Passed 0.26 sec +158/230 Test #166: testMMPA ............................... Passed 0.33 sec test 168 Start 168: testRascalMCES 168: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 168: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES 168: Test timeout computed to be: 1500 -139: [06:21:49] Rep: 80 Mol:2 -139: [06:21:49] Rep: 80 Mol:6 -139: [06:21:49] Rep: 80 Mol:10 -139: [06:21:49] Rep: 80 Mol:14 -139: [06:21:49] Rep: 80 Mol:18 -139: [06:21:49] Rep: 80 Mol:22 -139: [06:21:49] Rep: 80 Mol:26 -139: [06:21:49] Rep: 80 Mol:30 -141: [06:21:49] Rep: 100 Mol:0 -141: [06:21:49] Rep: 100 Mol:4 -141: [06:21:49] Rep: 100 Mol:8 -141: [06:21:49] Rep: 100 Mol:12 -141: [06:21:49] Rep: 100 Mol:16 -141: [06:21:49] Rep: 100 Mol:20 -141: [06:21:49] Rep: 100 Mol:24 -141: [06:21:49] Rep: 100 Mol:28 -115: =>start test AUTOCORR3D custom -115: [06:21:49] test on : 365 molecules done -147/230 Test #165: pyMolHash ..............................***Exception: SegFault 0.41 sec +159/230 Test #167: pyMMPA .................................***Exception: SegFault 0.35 sec test 169 Start 169: testRascalCluster @@ -31210,332 +31551,35 @@ 169: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 169: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES 169: Test timeout computed to be: 1500 -159: file rxn_test4_2.png gave hash 1540116253U not the expected 3490081297U -148/230 Test #167: pyMMPA .................................***Exception: SegFault 0.31 sec - +27: All 191 tests passed +27: done +27: ------------------------------------- +27: Unit tests for all MMFF constraint terms. +27: 10.0003 +144: validating reference data +27: done +27: ------------------------------------- +27: Unit test for MMFF TorsionConstraint close to 0 degrees. +27: done +27: ------------------------------------- +27: Unit tests for copying MMFF ForceFields. +27: done +27: ------------------------------------- +27: Unit test for MMFF butane scan. +158: file testHandDrawn-5a.svg gave hash 1742606296U not the expected 3628607349U +158: [02:44:15] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:15] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +27: done +160/230 Test #27: testMMFFForceField ..................... Passed 42.84 sec test 170 Start 170: pyRascalMCES 170: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 170: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap 170: Test timeout computed to be: 1500 -159: file rxn_test4_2.svg gave hash 3240313871U not the expected 2032588691U -159: Done -149/230 Test #159: moldraw2DRxnTest1 ...................... Passed 0.90 sec -test 171 - Start 171: testCIPLabeler - -171: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler -171: Test timeout computed to be: 1500 -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -141: [06:21:49] Rep: 100 Mol:1 -141: [06:21:49] Rep: 100 Mol:5 -141: [06:21:49] Rep: 100 Mol:9 -141: [06:21:49] Rep: 100 Mol:13 -141: [06:21:49] Rep: 100 Mol:17 -141: [06:21:49] Rep: 100 Mol:21 -141: [06:21:49] Rep: 100 Mol:25 -141: [06:21:49] Rep: 100 Mol:29 -171: Randomness seeded to: 3574153181 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -171: [06:21:49] non kekulizable aromatic bond being treated as bond order 1 -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -139: [06:21:49] done -139: [06:21:49] ------------------------------------- -139: [06:21:49] Test MMFF multithreading2 -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -115: =>start test 2 WHIM custom -115: [06:21:49] test on : 365 molecules done -145: [06:21:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -171: [06:21:50] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -171: [06:21:50] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -171: =============================================================================== -171: All tests passed (6572 assertions in 18 test cases) -171: -150/230 Test #170: pyRascalMCES ...........................***Exception: SegFault 0.57 sec - -151/230 Test #171: testCIPLabeler ......................... Passed 0.54 sec -test 172 - Start 172: pyCIPLabelsWrapTest - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" -172: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -172: Test timeout computed to be: 1500 -test 173 - Start 173: pyCIPLabelsValidation - -173: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" -173: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -173: Test timeout computed to be: 1500 -144: [06:21:47] --------------------------------- -144: [06:21:47] test3 -144: -144: [06:21:47] --------------------------------- -144: [06:21:47] test4 -144: -144: [06:21:47] --------------------------------- -144: [06:21:47] test5 -144: -144: [06:21:49] --------------------------------- -144: [06:21:49] test6 -144: -144: [06:21:49] --------------------------------- -144: [06:21:49] test15Dists -144: -144: [06:21:49] --------------------------------- -144: [06:21:49] test Issue 215 -144: -144: [06:21:49] --------------------------------- -144: [06:21:49] testMultipleConfs -144: -144: [06:21:49] --------------------------------- -144: [06:21:49] testMultipleConfsExpTors -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue227 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue236 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testOrdering -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue244 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue251 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue276 -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue284 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue285 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testIssue355 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] testRandomCoords -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 1989539 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 2091864 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test constrained embedding -144: -144: [06:21:50] ssd: 0.0752641 -144: [06:21:50] ssd: 0.0659363 -115: =>start test 1 WHIM custom -115: [06:21:50] test on : 365 molecules done -139: [06:21:50] done -139: [06:21:50] ------------------------------------- -139: [06:21:50] Test MMFF multithreading3 -152/230 Test #172: pyCIPLabelsWrapTest ....................***Exception: SegFault 0.33 sec - -test 174 - Start 174: deprotectTest - -174: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest -174: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect -174: Test timeout computed to be: 1500 -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 2091974 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 2835784 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 3019283 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 3238580 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test sf.net issue 3483968 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test github issue 55 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test1 -144: -144: [06:21:50] --------------------------------- -144: [06:21:50] test multi-threading -144: -144: building molecules -144: generating reference data -149: 2527823762 -174: Randomness seeded to: 1013641749 -174: =============================================================================== -174: All tests passed (111 assertions in 3 test cases) -174: -153/230 Test #174: deprotectTest .......................... Passed 0.30 sec -test 175 - Start 175: pyDeprotect - -175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/rough_test.py" -175: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap -175: Test timeout computed to be: 1500 -154/230 Test #173: pyCIPLabelsValidation ..................***Exception: SegFault 0.65 sec - -test 176 - Start 176: testReducedGraphs - -176: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -176: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs -176: Test timeout computed to be: 1500 -141: [06:21:50] done -141: [06:21:50] ------------------------------------- -141: [06:21:50] Test UFF multithreading2 -176: 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, 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0.3, 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, 0.3, 1, 0.3, 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, 0.3, 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, ] -176: -176: 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, ] -176: -155/230 Test #176: testReducedGraphs ...................... Passed 0.06 sec -test 177 - Start 177: pyReducedGraphs - -177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -177: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -177: Test timeout computed to be: 1500 -156/230 Test #175: pyDeprotect ............................***Exception: SegFault 0.89 sec - -test 178 - Start 178: trajectoryTest - -178: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory -178: Test timeout computed to be: 1500 -157/230 Test #177: pyReducedGraphs ........................***Exception: SegFault 0.84 sec - -test 179 - Start 179: substructLibraryTest - -179: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary -179: Test timeout computed to be: 1500 -179: [06:21:51] ------------------------------------- -179: [06:21:51] Test1 -158: file testHandDrawn-5a.svg gave hash 1742606296U not the expected 3628607349U -158: [06:21:51] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:51] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test unfolded version of RDKFP -126: [06:21:51] ------------------------------------- -126: [06:21:51] Test bitinfo of RDKFP -126: 562: [ 2 ], -126: 709: [ 0 1 ], -126: 1118: [ 0 1 2 ], -126: 1183: [ 1 2 ], -126: 1233: [ 0 1 2 ], -126: 1308: [ 0 ], [ 1 ], -126: 1339: [ 2 ], -126: 1728: [ 1 2 ], -126: 1772: [ 0 ], [ 1 ], 158: file testHandDrawn-5b.svg gave hash 2290757626U not the expected 2522138089U -158: [06:21:51] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [06:21:51] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -126: 1813: [ 0 1 ], -126: ------------ -126: [06:21:51] ------------------------------------- -126: [06:21:51] Single atoms setting radius 1 bits in Morgan fingerprints -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #879: Pattern fingerprint should set bits for single-atom fragments. -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use AtomPairGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #2115: BitInfo not complete for RDKFingerprint -126: [06:21:51] done -126: [06:21:51] ------------------------------------- -126: [06:21:51] Github #3723: Fingerprint crash for mols with Zero order bonds -126: [06:21:51] done -158/230 Test #126: testFingerprints ....................... Passed 5.88 sec -test 180 - Start 180: substructLibraryCatchTest - -180: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary -180: Test timeout computed to be: 1500 +158: [02:44:15] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [02:44:15] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-5.png gave hash 1137148752U not the expected 3439548169U 158: file testBrackets-1a.svg gave hash 2369751903U not the expected 4189399574U 158: file testBrackets-1b.svg gave hash 319778462U not the expected 3773894816U @@ -31547,13 +31591,6 @@ 158: file testBrackets-2c.svg gave hash 3500488585U not the expected 1050851904U 158: file testBrackets-2d.svg gave hash 2920281586U not the expected 776446765U 158: file testBrackets-3a.svg gave hash 28453276U not the expected 1374944956U -159/230 Test #178: trajectoryTest ......................... Passed 0.44 sec -test 181 - Start 181: pySubstructLibrary - -181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -181: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -181: Test timeout computed to be: 1500 158: file testBrackets-4a.svg gave hash 194812969U not the expected 3837821771U 158: file testBrackets-4b.svg gave hash 1005379322U not the expected 1477006167U 158: file testBrackets-5a.svg gave hash 770135436U not the expected 3061667963U @@ -31565,15 +31602,6 @@ 158: file testSGroupData-2b.svg gave hash 1776709036U not the expected 942041938U 158: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U 158: file testPositionVariation-1.svg gave hash 175752745U not the expected 1347003808U -139: [06:21:52] done -139: [06:21:52] ------------------------------------- -139: [06:21:52] Testing github 162: Incorrect SMILES after MMFF parameterization . -139: [06:21:52] done -139: [06:21:52] ------------------------------------- -139: [06:21:52] Testing github 224: crash during MMFF parameterization . -139: [06:21:52] done -139: [06:21:52] ------------------------------------- -139: [06:21:52] Testing github6728: crash due to missing stretch-bend params. 158: file testPositionVariation-1b.svg gave hash 1587871191U not the expected 174339626U 158: file testPositionVariation-2.svg gave hash 3363492135U not the expected 473948585U 158: file testPositionVariation-3.svg gave hash 3172212082U not the expected 4039188982U @@ -31581,13 +31609,6 @@ 158: file testNoAtomLabels-1.svg gave hash 727719523U not the expected 4255907058U 158: file testNoAtomLabels-2.svg gave hash 4176633817U not the expected 3643749531U 158: file testQueryBonds-1a.svg gave hash 1498812112U not the expected 1525751327U -160/230 Test #139: testMMFFForceFieldHelpers .............. Passed 5.41 sec -test 182 - Start 182: testRGroupDecomp - -182: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -182: Test timeout computed to be: 1500 158: file testQueryBonds-1b.svg gave hash 1854448352U not the expected 3339941561U 158: file testQueryBonds-1c.svg gave hash 1282788757U not the expected 375371096U 158: file testQueryBonds-2.svg gave hash 176419118U not the expected 3399320861U @@ -31598,40 +31619,93 @@ 158: file testLinkNodes-2-120.svg gave hash 3176047424U not the expected 673333745U 158: file testLinkNodes-2-150.svg gave hash 4108663686U not the expected 51965551U 158: file testLinkNodes-2-180.svg gave hash 1267063813U not the expected 433020402U +158: file testMolAnnotations-1.svg gave hash 4022064522U not the expected 1638024035U +158: file testMolAnnotations-2a.svg gave hash 100295044U not the expected 3029896996U +158: file testMolAnnotations-2b.svg gave hash 1729540304U not the expected 3110016833U +158: file testMolAnnotations-2c.svg gave hash 3114393753U not the expected 611992302U +158: file testMolAnnotations-3a.svg gave hash 1578731737U not the expected 55379064U +158: file testMolAnnotations-3b.svg gave hash 3914185508U not the expected 936144383U +158: file testMolAnnotations-3c.svg gave hash 613361257U not the expected 3983292921U +158: file testMolAnnotations-3d.svg gave hash 3911959820U not the expected 748075045U +158: file testMolAnnotations-4a.svg gave hash 3377859254U not the expected 3474490519U +158: file testLinkNodes-1-0.svg gave hash 132913310U not the expected 3845035394U +158: file testLinkNodes-1-30.svg gave hash 4167789299U not the expected 3207457801U +158: file testLinkNodes-1-60.svg gave hash 3654538383U not the expected 2620138210U +158: file testLinkNodes-1-90.svg gave hash 2745010131U not the expected 1457485851U +158: file testLinkNodes-1-120.svg gave hash 486328858U not the expected 4267267665U +158: file testLinkNodes-1-150.svg gave hash 3641412484U not the expected 574622776U +158: file testLinkNodes-1-180.svg gave hash 2073805227U not the expected 2541146503U +158: file testGithub3744.svg gave hash 829939430U not the expected 387800653U +158: file testAtomLists-1.svg gave hash 3464470154U not the expected 1887579391U +158: file testAtomLists-2.svg gave hash 802804202U not the expected 555139782U +158: file testIsoDummyIso.svg gave hash 1524400075U not the expected 2405371137U +158: file testNoIsoDummyIso.svg gave hash 3628257665U not the expected 748558214U +158: file testIsoNoDummyIso.svg gave hash 3076357258U not the expected 3054263824U +158: file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U +158: file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U +158: file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U +158: [02:44:16] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U +158: file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U +158: file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U +158: file testGithub2976.svg gave hash 968668044U not the expected 2669316911U +158: file testReactionCoords.svg gave hash 1202163015U not the expected 402445764U +158: file testAnnotationColors.svg gave hash 1685962958U not the expected 2216313312U +158: file testGithub4238_1.svg gave hash 2002583221U not the expected 2621118499U +158: file testGithub4238_1.png gave hash 74980557U not the expected 3410617836U +158: file testGithub4323_1.svg gave hash 2366752113U not the expected 2536621192U +158: file testGithub4323_2.svg gave hash 2788649217U not the expected 2120846759U +158: file testGithub4323_3.svg gave hash 2889173297U not the expected 4156867630U +158: file testGithub4323_4.svg gave hash 1561706994U not the expected 3824125601U +158: file testGithub4323_1.png gave hash 1246412143U not the expected 3723958844U +161/230 Test #170: pyRascalMCES ...........................***Exception: SegFault 0.99 sec + +test 171 + Start 171: testCIPLabeler + +171: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler +171: Test timeout computed to be: 1500 +171: Randomness seeded to: 3030432009 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 +171: [02:44:16] non kekulizable aromatic bond being treated as bond order 1 161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 161: Time elapsed 0.001 seconds 161: 161: test32() 161: 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 -161: Time elapsed 0.124 seconds +161: Time elapsed 0.139 seconds 161: 161: test190() 161: 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 -161: Time elapsed 0.023 seconds +161: Time elapsed 0.015 seconds 161: 161: test3() 161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -161: Time elapsed 0.020 seconds +161: Time elapsed 0.021 seconds 161: 161: testSimpleFast() 161: 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 -161: Time elapsed 0.143 seconds +161: Time elapsed 0.180 seconds 161: 161: testSimple() 161: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.107 seconds +161: Time elapsed 0.185 seconds 161: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.175 seconds +161: Time elapsed 0.282 seconds 161: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.129 seconds +161: Time elapsed 0.191 seconds 161: 161: testSegFault() 161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.012 seconds +161: Time elapsed 0.014 seconds 161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.017 seconds +161: Time elapsed 0.019 seconds 161: 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 -161: Time elapsed 0.016 seconds +161: Time elapsed 0.020 seconds 161: 161: testThreshold() 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -31639,15 +31713,15 @@ 161: 161: testRing1() 161: 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 -161: Time elapsed 0.808 seconds +161: Time elapsed 0.471 seconds 161: 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 -161: Time elapsed 1.264 seconds +161: Time elapsed 0.577 seconds 161: 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 -161: Time elapsed 0.466 seconds +161: Time elapsed 1.366 seconds 161: 161: testAtomCompareIsotopes() 161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -161: Time elapsed 0.008 seconds +161: Time elapsed 0.012 seconds 161: 161: testAtomCompareAnyAtom() 161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds @@ -31667,68 +31741,29 @@ 161: 161: testJnk1LigandsDistance() 161: 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 -161: Time elapsed 0.011 seconds +161: Time elapsed 0.016 seconds 161: 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 -158: file testMolAnnotations-1.svg gave hash 4022064522U not the expected 1638024035U -158: file testMolAnnotations-2a.svg gave hash 100295044U not the expected 3029896996U -158: file testMolAnnotations-2b.svg gave hash 1729540304U not the expected 3110016833U -158: file testMolAnnotations-2c.svg gave hash 3114393753U not the expected 611992302U -158: file testMolAnnotations-3a.svg gave hash 1578731737U not the expected 55379064U -158: file testMolAnnotations-3b.svg gave hash 3914185508U not the expected 936144383U -158: file testMolAnnotations-3c.svg gave hash 613361257U not the expected 3983292921U -158: file testMolAnnotations-3d.svg gave hash 3911959820U not the expected 748075045U -158: file testMolAnnotations-4a.svg gave hash 3377859254U not the expected 3474490519U -158: file testLinkNodes-1-0.svg gave hash 132913310U not the expected 3845035394U -158: file testLinkNodes-1-30.svg gave hash 4167789299U not the expected 3207457801U -158: file testLinkNodes-1-60.svg gave hash 3654538383U not the expected 2620138210U -158: file testLinkNodes-1-90.svg gave hash 2745010131U not the expected 1457485851U -179: [06:21:52] done -158: file testLinkNodes-1-120.svg gave hash 486328858U not the expected 4267267665U -158: file testLinkNodes-1-150.svg gave hash 3641412484U not the expected 574622776U -158: file testLinkNodes-1-180.svg gave hash 2073805227U not the expected 2541146503U -158: file testGithub3744.svg gave hash 829939430U not the expected 387800653U -179: [06:21:52] ------------------------------------- -158: file testAtomLists-1.svg gave hash 3464470154U not the expected 1887579391U -158: file testAtomLists-2.svg gave hash 802804202U not the expected 555139782U -158: file testIsoDummyIso.svg gave hash 1524400075U not the expected 2405371137U -158: file testNoIsoDummyIso.svg gave hash 3628257665U not the expected 748558214U -158: file testIsoNoDummyIso.svg gave hash 3076357258U not the expected 3054263824U -179: [06:21:52] Test2 -158: file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U -158: file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U -158: file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U -158: [06:21:52] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U -158: file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U -158: file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U -158: file testGithub2976.svg gave hash 968668044U not the expected 2669316911U -158: file testReactionCoords.svg gave hash 1202163015U not the expected 402445764U -158: file testAnnotationColors.svg gave hash 1685962958U not the expected 2216313312U -158: file testGithub4238_1.svg gave hash 2002583221U not the expected 2621118499U -158: file testGithub4238_1.png gave hash 74980557U not the expected 3410617836U -158: file testGithub4323_1.svg gave hash 2366752113U not the expected 2536621192U -158: file testGithub4323_2.svg gave hash 2788649217U not the expected 2120846759U -158: file testGithub4323_3.svg gave hash 2889173297U not the expected 4156867630U -158: file testGithub4323_4.svg gave hash 1561706994U not the expected 3824125601U -158: file testGithub4323_1.png gave hash 1246412143U not the expected 3723958844U -161: Time elapsed 0.002 seconds +171: [02:44:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +171: [02:44:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +161: Time elapsed 0.003 seconds 161: 161: test18() 161: 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]1 161: 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 -161: Time elapsed 0.006 seconds +161: Time elapsed 0.012 seconds 161: 161: test504() 161: 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]1 161: 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 -161: Time elapsed 0.100 seconds +161: Time elapsed 0.173 seconds 161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -161: Time elapsed 0.002 seconds +161: Time elapsed 0.003 seconds 161: 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 -161: Time elapsed 0.035 seconds +161: Time elapsed 0.079 seconds 161: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -161: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0012 seconds. bond[0]=6 +161: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0013 seconds. bond[0]=6 161: STATISTICS: -161: Total Growing Steps = 1, MCS found on 1 step, for 0.0012 seconds +161: Total Growing Steps = 1, MCS found on 1 step, for 0.0013 seconds 161: Initial Seeds = 1, Mismatched 0 161: Inspected Seeds = 2 161: Rejected by BestSize = 0 @@ -31747,7 +31782,7 @@ 161: HashFoundInCache= 0 161: ExactMatchCalls = 0 161: ExactMatchFound = 0 -161: Time elapsed 0.002 seconds +161: Time elapsed 0.009 seconds 161: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 161: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 161: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 @@ -31843,68 +31878,50 @@ 161: res sub = 1 size=3 161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 161: done -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -141: [06:21:52] done -141: [06:21:52] ------------------------------------- -141: [06:21:52] Test UFF multithreading3 -149: 1664393532 -149: =============================================================================== -149: All tests passed (73 assertions in 3 test cases) -149: -161/230 Test #149: molAlignCatchTest ...................... Passed 4.59 sec -test 183 - Start 183: testRGroupDecompInternals - -183: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -183: Test timeout computed to be: 1500 -162/230 Test #181: pySubstructLibrary .....................***Exception: SegFault 0.51 sec - -test 184 - Start 184: rgroupCatchTests - -184: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -184: Test timeout computed to be: 1500 -179: [06:21:52] done -179: [06:21:52] ------------------------------------- -179: [06:21:52] Test3 (stereo options) -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [06:21:52] WARNING: not removing hydrogen atom with dummy atom neighbors -163/230 Test #183: testRGroupDecompInternals .............. Passed 0.09 sec -test 185 - Start 185: pyRGroupDecomposition +171: =============================================================================== +171: All tests passed (6572 assertions in 18 test cases) +171: +162/230 Test #171: testCIPLabeler ......................... Passed 0.80 sec +test 172 + Start 172: pyCIPLabelsWrapTest -185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" -185: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap -185: Test timeout computed to be: 1500 -27: All 191 tests passed +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" +172: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +172: Test timeout computed to be: 1500 158: file testGithub4323_3.png gave hash 2266718033U not the expected 2185913679U 158: file testGithub4508_1.svg gave hash 3378775316U not the expected 2047652713U -158: [06:21:52] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +158: [02:44:17] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 158: file testGithub4508_1b.svg gave hash 860872304U not the expected 2681019776U -179: [06:21:52] Done (stereo options) -179: [06:21:52] ------------------------------------- -179: [06:21:52] Test4 (trusted smiles) +148: *********************************************************** +148: Testing O3AAlign +148: --------------------------------- +148: testMMFFO3A +148: +148: --------------------------------- +148: testMMFFO3A with pre-computed dmat and MolHistogram +148: +148: --------------------------------- +148: testMMFFO3A with constraints +148: +148: --------------------------------- +148: testMMFFO3A with variable weight constraints followed by local-only optimization +148: +148: --------------------------------- +148: testCrippenO3A +148: +148: --------------------------------- +148: testCrippenO3A with pre-computed dmat and MolHistogram +148: +148: --------------------------------- +148: testCrippenO3A with constraints +148: +148: --------------------------------- +148: testCrippenO3A with variable weight constraints followed by local-only optimization +148: +148: --------------------------------- +148: testMMFFO3A multithreading +148: +148: generating reference data 158: file testGithub4508_2.svg gave hash 1943409269U not the expected 1382076550U 158: file testGithub4508_2b.svg gave hash 1021344995U not the expected 4005636724U 158: file testGithub4538.svg gave hash 1030251935U not the expected 2797362550U @@ -31914,89 +31931,27 @@ 158: file testAvalon.1.svg gave hash 447120226U not the expected 477303888U 158: file testCDK.1.svg gave hash 3760150813U not the expected 1764612361U 158: file testGithub4519_1.svg gave hash 3038145453U not the expected 736612670U +163/230 Test #172: pyCIPLabelsWrapTest ....................***Exception: SegFault 0.40 sec + +test 173 + Start 173: pyCIPLabelsValidation + +173: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" +173: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +173: Test timeout computed to be: 1500 158: file testGithub4519_2.svg gave hash 3134958419U not the expected 171503813U 158: file testGithub4519_3.svg gave hash 2970193890U not the expected 3396792960U 158: file testGithub4519_4.svg gave hash 111372964U not the expected 3924693257U -179: [06:21:53] Done (trusted smiles) -179: [06:21:53] ------------------------------------- -179: [06:21:53] Testing C++ docs -179: [06:21:53] Done (C++ doc tests) -179: [06:21:53] ------------------------------------- -179: [06:21:53] Testing C++ ring query: PatternHolder -179: [06:21:53] Done (C++ ring query tests) -179: [06:21:53] ------------------------------------- -179: [06:21:53] Testing C++ ring query: TautomerPatternHolder -179: [06:21:53] Done (C++ ring query tests) -179: [06:21:53] ------------------------------------- -179: [06:21:53] Add Patterns -164/230 Test #185: pyRGroupDecomposition ..................***Exception: SegFault 0.34 sec - -test 186 - Start 186: molInterchangeTest1 - -186: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 -186: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange -186: Test timeout computed to be: 1500 -186: [06:21:53] test1: basics -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 158: file testBaseFontSize.1a.svg gave hash 4001693957U not the expected 1295117205U -182: [06:21:53] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [06:21:53] done -186: [06:21:53] test2: basic writing -186: {"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":"2024.09.2","cipRanks":[0,0]}]}]} -186: {"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":"2024.09.2","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} -186: {"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":"2024.09.2","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]]}]}]} -186: {"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":"2024.09.2","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]]}]}]} -186: [06:21:53] done -186: [06:21:53] test3: writing conformers -186: {"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":"2024.09.2","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -186: [06:21:53] done -186: [06:21:53] test4: writing properties -186: {"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":"2024.09.2","cipRanks":[0,0]}]}]} -186: [06:21:53] done -186: [06:21:53] test5: writing partial charges -186: {"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":"2024.09.2","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[0.5,-0.5]}]}]} -186: [06:21:53] testing parse options -186: [06:21:53] done -186: [06:21:53] testing github #2046: CIPRank values from JSONDataToMols are not unsigned -186: {"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":"2024.09.2","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -186: [06:21:53] done -186: [06:21:53] testing 'either' stereochemistry -186: [06:21:53] done -165/230 Test #186: molInterchangeTest1 .................... Passed 0.11 sec -test 187 - Start 187: molInterchangeCatchTest - -187: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest -187: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange -187: Test timeout computed to be: 1500 -182: [06:21:53] WARNING: not removing hydrogen atom with dummy atom neighbors -187: Randomness seeded to: 2031242884 -187: [06:21:53] unrecognized bond type 12 set to zero while writing -187: [06:21:53] unrecognized bond type 0 set to zero while writing -187: =============================================================================== -187: All tests passed (122 assertions in 6 test cases) -187: 158: file testBaseFontSize.1b.svg gave hash 4281598149U not the expected 3595811515U -166/230 Test #187: molInterchangeCatchTest ................ Passed 0.05 sec -test 188 - Start 188: pyMolInterchange +164/230 Test #173: pyCIPLabelsValidation ..................***Exception: SegFault 0.51 sec -188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" -188: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap -188: Test timeout computed to be: 1500 -184: Randomness seeded to: 4181134857 -184: =============================================================================== -184: All tests passed (1475 assertions in 14 test cases) -184: -167/230 Test #184: rgroupCatchTests ....................... Passed 0.63 sec -test 189 - Start 189: testSLNParse +test 174 + Start 174: deprotectTest -189: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse/testSLNParse -189: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse -189: Test timeout computed to be: 1500 +174: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest +174: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect +174: Test timeout computed to be: 1500 158: ------------------------------------------------------------------------------- 158: changing baseFontSize 158: basics-small @@ -32010,64 +31965,23 @@ 158: 13.8691064544746343 == Approx( 14.0 ) 158: 158: file testBaseFontSize.2a.svg gave hash 4236623323U not the expected 2958687877U -141: [06:21:53] done -141: [06:21:53] ------------------------------------- -141: [06:21:53] Testing GitHubIssue62. -141: [06:21:53] beta-lactam 39.6387 -141: [06:21:53] cyclopropanone 174.698 -141: [06:21:53] aziridine 337.986 -141: [06:21:53] aziridinone 115.248 -141: [06:21:53] isobutene 2.48217 -141: [06:21:53] acetone 1.91788 -141: [06:21:53] cyclopentanone 10.1648 -141: [06:21:53] cyclopropene 99.4921 -141: [06:21:53] cyclobutene 41.0156 -141: [06:21:53] cyclopropane 267.236 -141: [06:21:53] gamma-lactam 15.7471 158: file testBaseFontSize.2b.svg gave hash 3431978475U not the expected 1786972332U -189: Atoms: -189: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: -189: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -189: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -189: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -189: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -189: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: -189: Bonds: -189: 0 0->1 order: 1 -189: 1 0->2 order: 1 -189: 2 0->3 order: 1 -189: 3 0->4 order: 1 -189: 4 0->5 order: 1 -189: [06:21:53] SLN Parse Error: syntax error while parsing: CH4[I=13] -189: [06:21:53] Failed parsing SLN 'CH4[I=13]' -141: [06:21:53] trans-2,3-diphenylcyclopropan-1-one 203.398 -189: [06:21:53] SLN Parser error: Atom ID 1 appears *after* its ring closure. -189: [06:21:53] SLN Parser error: Ring closure 1 does not have a corresponding opener. -189: [06:21:53] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -189: [06:21:53] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -189: [06:21:53] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -189: [06:21:53] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -189: [06:21:53] SLN Parse Error: syntax error while parsing: CH4 fff -189: [06:21:53] Failed parsing SLN 'CH4 fff' -189: [06:21:53] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -189: [06:21:53] Failed parsing SLN 'C[charge=+1] foo' +174: Randomness seeded to: 3551962699 +174: =============================================================================== +174: All tests passed (111 assertions in 3 test cases) +174: +165/230 Test #174: deprotectTest .......................... Passed 0.25 sec +test 175 + Start 175: pyDeprotect + +175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/rough_test.py" +175: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap +175: Test timeout computed to be: 1500 158: file testFlexiCanvas.2.svg gave hash 3528076106U not the expected 665664909U 158: file testFlexiCanvas.2a.png gave hash 4288280796U not the expected 3217758043U 158: file testFlexiCanvas.2b.png gave hash 3583431125U not the expected 4070063910U -189: [06:21:53] Query property 'is' ignored on non-query atom -189: [06:21:53] Query property 'is' ignored on non-query atom -168/230 Test #189: testSLNParse ........................... Passed 0.11 sec -test 190 - Start 190: pySLNParse - -190: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/Wrap/testSLN.py" -190: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap -190: Test timeout computed to be: 1500 158: file testSemiFlexiCanvas.1c.svg gave hash 1887143568U not the expected 4178696811U 158: file testFlexiCanvas.3.svg gave hash 1498773600U not the expected 2819587550U -141: [06:21:53] cis-2,3-diphenylcyclopropan-1-one 206.852 -141: [06:21:53] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -141: [06:21:53] cyclopropylidencyclobutane 218.879 158: file testFlexiCanvas.6a.svg gave hash 3710806917U not the expected 3085867303U 158: file testFlexiCanvas.6b.svg gave hash 4179603074U not the expected 2819164642U 158: file testFlexiCanvas.6c.svg gave hash 3710806917U not the expected 3085867303U @@ -32077,52 +31991,10 @@ 158: file testFlexiCanvas.7c.svg gave hash 128018593U not the expected 514767495U 158: file testFlexiCanvas.7d.svg gave hash 128018593U not the expected 514767495U 158: file testGithub4764.sz1.svg gave hash 2950365870U not the expected 3611125861U -141: [06:21:53] diphenylmethylidencyclobutane 79.6139 -141: [06:21:53] done -141: [06:21:53] ------------------------------------- -141: [06:21:53] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -141: [06:21:53] done -141: [06:21:53] ------------------------------------- -141: [06:21:53] Test square planar complexes -141: [06:21:53] done -141: [06:21:53] ------------------------------------- -141: [06:21:53] Test octahedral complexes -141: [06:21:53] done 158: file testGithub4764.sz2.svg gave hash 1059315367U not the expected 1936114454U 158: file testGithub4764.sz3.svg gave hash 157477816U not the expected 2712214121U -169/230 Test #141: testUFFForceFieldHelpers ............... Passed 6.42 sec -170/230 Test #188: pyMolInterchange .......................***Exception: SegFault 0.28 sec - -test 191 - Start 191: pyGraphMolWrap - -191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rough_test.py" -191: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -191: Test timeout computed to be: 1500 -test 192 - Start 192: pyTestConformerWrap - -192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testConformer.py" -192: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -192: Test timeout computed to be: 1500 158: file testGithub4764.sz1.png gave hash 3487048786U not the expected 98827714U 158: file testGithub4764.sz2.png gave hash 3070603363U not the expected 89252465U -180: Randomness seeded to: 378510404 -180: =============================================================================== -180: All tests passed (171 assertions in 5 test cases) -180: -171/230 Test #180: substructLibraryCatchTest .............. Passed 1.54 sec -test 193 - Start 193: pyTestTrajectory - -193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testTrajectory.py" -193: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -193: Test timeout computed to be: 1500 -73: [06:21:53] Finished: testSmiCorrectness() -73: [06:21:53] ----------------------------------------- -73: -73: [06:21:53] -73: ----------------------------------------- 158: file testGithub4764.sz3.png gave hash 1694311270U not the expected 148503574U 158: file testDrawArc1.svg gave hash 693243455U not the expected 3279637525U 158: file testMetalWedges.svg gave hash 2458660191U not the expected 2896721486U @@ -32180,10 +32052,6 @@ 158: file github5383_2.svg gave hash 2780318590U not the expected 0U 158: file github5383_1.png gave hash 1227747953U not the expected 992803933U 158: file github5156_1.svg gave hash 721047374U not the expected 2145907703U -73: [06:21:53] Spurious data before the first property will be ignored -73: [06:21:53] Property will be truncated after the first blank line -73: [06:21:53] Property will be truncated after the first blank line -73: [06:21:53] Property will be truncated after the first blank line 158: file github5156_2.svg gave hash 1299449958U not the expected 4184795863U 158: file github5156_3.svg gave hash 1955608996U not the expected 420595965U 158: file acs1996_1.png gave hash 342575424U not the expected 2957839025U @@ -32197,7 +32065,7 @@ 158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U 158: file acs1996_10.svg gave hash 3594677893U not the expected 2229333301U 158: file acs1996_11.svg gave hash 3362983424U not the expected 4107969968U -158: [06:21:53] 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. +158: [02:44:18] 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. 158: file acs1996_12.svg gave hash 3867577622U not the expected 2930884583U 158: file test_unspec_stereo.svg gave hash 2773708102U not the expected 3923423666U 158: file light_blue_h_no_label_1.svg gave hash 1500404507U not the expected 1615074554U @@ -32207,14 +32075,6 @@ 158: file bond_highlights_4.svg gave hash 3375036480U not the expected 851066096U 158: file bond_highlights_5.svg gave hash 4265482767U not the expected 2352169547U 158: file bond_highlights_6.svg gave hash 1430730331U not the expected 2125370009U -172/230 Test #190: pySLNParse .............................***Exception: SegFault 0.33 sec - -test 194 - Start 194: pyTestSGroups - -194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testSGroups.py" -194: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -194: Test timeout computed to be: 1500 158: file bond_highlights_8.svg gave hash 4239480016U not the expected 2956924065U 158: file bond_highlights_9.svg gave hash 1043957016U not the expected 3999278931U 158: file testGithub5486_1.svg gave hash 634992317U not the expected 3146085634U @@ -32313,22 +32173,6 @@ 158: file test_complex_query_atoms_2.svg gave hash 1906356409U not the expected 3820627663U 158: file test_complex_query_atoms_3.svg gave hash 3168710914U not the expected 2574610745U 158: file test_complex_query_atoms_4.svg gave hash 3168710914U not the expected 2574610745U -173/230 Test #192: pyTestConformerWrap ....................***Exception: SegFault 0.34 sec - -174/230 Test #193: pyTestTrajectory .......................***Exception: SegFault 0.30 sec - -test 195 - Start 195: pyTestThreads - -195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testThreads.py" -195: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -195: Test timeout computed to be: 1500 -test 196 - Start 196: pyTestMultithreadedMolSupplier - -196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -196: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -196: Test timeout computed to be: 1500 158: file test_complex_query_atoms_5.svg gave hash 371718771U not the expected 2239402605U 158: file test_complex_query_atoms_6.svg gave hash 1721346649U not the expected 2784917732U 158: file test_complex_query_atoms_7.svg gave hash 3692574947U not the expected 4016570948U @@ -32342,36 +32186,6 @@ 158: file test_complex_query_atoms_15.svg gave hash 2920839489U not the expected 422354297U 158: file test_complex_query_atoms_16.svg gave hash 1393033379U not the expected 1559600050U 158: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -148: *********************************************************** -148: Testing O3AAlign -148: --------------------------------- -148: testMMFFO3A -148: -148: --------------------------------- -148: testMMFFO3A with pre-computed dmat and MolHistogram -148: -148: --------------------------------- -148: testMMFFO3A with constraints -148: -148: --------------------------------- -148: testMMFFO3A with variable weight constraints followed by local-only optimization -148: -148: --------------------------------- -148: testCrippenO3A -148: -148: --------------------------------- -148: testCrippenO3A with pre-computed dmat and MolHistogram -148: -148: --------------------------------- -148: testCrippenO3A with constraints -148: -148: --------------------------------- -148: testCrippenO3A with variable weight constraints followed by local-only optimization -148: -148: --------------------------------- -148: testMMFFO3A multithreading -148: -148: generating reference data 158: file test_github6160_1.svg gave hash 665570952U not the expected 518073509U 158: file test_github6160_2.svg gave hash 3180863814U not the expected 2491651948U 158: file test_github6160_3.svg gave hash 286670546U not the expected 2709442517U @@ -32401,6 +32215,14 @@ 158: 257.39999999999997726 is within 0.10000000000000001 of 258.30000000000001137 158: 158: file test_github6397_3.svg gave hash 389909808U not the expected 3320683230U +166/230 Test #175: pyDeprotect ............................***Exception: SegFault 0.69 sec + +test 176 + Start 176: testReducedGraphs + +176: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +176: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs +176: Test timeout computed to be: 1500 158: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:7786: FAILED: 158: CHECK_THAT( y, Catch::Matchers::WithinAbs(expY, 0.1) ) 158: with expansion: @@ -32430,14 +32252,8 @@ 158: 271.60000000000002274 is within 0.10000000000000001 of 272.10000000000002274 158: 158: file lasso_highlights_1.svg gave hash 3008191139U not the expected 3709434534U -175/230 Test #194: pyTestSGroups ..........................***Exception: SegFault 0.28 sec - -test 197 - Start 197: pyTestPropertyLists - -197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testPropertyLists.py" -197: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 +176: 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +176: 158: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:8276: FAILED: 158: CHECK_THAT( stod(dat1[1]), Catch::Matchers::WithinAbs(389.5, 0.1) ) 158: with expansion: @@ -32449,6 +32265,18 @@ 158: 389.69999999999998863 is within 0.10000000000000001 of 390.19999999999998863 158: 158: file lasso_highlights_2.svg gave hash 2768847802U not the expected 757121560U +176: Size: 315 [ 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, 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244.69999999999998863 is within 0.10000000000000001 of 245.19999999999998863 158: 158: file lasso_highlights_3.svg gave hash 385384887U not the expected 556406365U +176: 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, 0.3, 1, 0.3, 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, 0.3, 1, 0.3, 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, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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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, ] +176: 158: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:8374: FAILED: 158: CHECK_THAT( stod(dat1[1]), Catch::Matchers::WithinAbs(223.2, 0.1) ) 158: with expansion: @@ -32500,15 +32332,14 @@ 158: with expansion: 158: 245.0 is within 0.10000000000000001 of 245.5 158: -158: file lasso_highlights_4.svg gave hash 1355104698U not the expected 4148844874U -176/230 Test #191: pyGraphMolWrap .........................***Exception: SegFault 0.55 sec - -test 198 - Start 198: pyCDXMLTest +167/230 Test #176: testReducedGraphs ...................... Passed 0.14 sec +test 177 + Start 177: pyReducedGraphs -198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/test_cdxml.py" -198: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap -198: Test timeout computed to be: 1500 +177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +177: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +177: Test timeout computed to be: 1500 +158: file lasso_highlights_4.svg gave hash 1355104698U not the expected 4148844874U 158: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:8433: FAILED: 158: CHECK_THAT( stod(dat1[1]), Catch::Matchers::WithinAbs(223.2, 0.1) ) 158: with expansion: @@ -32552,9 +32383,6 @@ 158: 247.69999999999998863 is within 0.10000000000000001 of 248.19999999999998863 158: 158: file lasso_highlights_7.svg gave hash 3849299004U not the expected 514868036U -73: [06:21:54] Finished: testSDCorrectness() -73: [06:21:54] ----------------------------------------- -73: 158: ./Code/GraphMol/MolDraw2D/catch_tests.cpp:8713: FAILED: 158: CHECK_THAT( stod(dat1[2]), Catch::Matchers::WithinAbs(318.1, 0.1) ) 158: with expansion: @@ -32565,100 +32393,13 @@ 158: with expansion: 158: 320.5 is within 0.10000000000000001 of 320.69999999999998863 158: -177/230 Test #73: testMultithreadedMolSupplier ........... Passed 10.30 sec -test 199 - Start 199: molStandardizeTest - -199: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -199: Test timeout computed to be: 1500 158: file lasso_highlights_8.svg gave hash 3429247564U not the expected 3231367552U -178/230 Test #195: pyTestThreads ..........................***Exception: SegFault 0.29 sec - -test 200 - Start 200: molNormalizeTest - -200: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -200: Test timeout computed to be: 1500 -179/230 Test #196: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.30 sec - -test 201 - Start 201: molValidateTest - -201: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -201: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -201: Test timeout computed to be: 1500 -200: [06:21:54] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 158: file bad_lasso_1.svg gave hash 2963562651U not the expected 726527516U 158: file AtropCanon1.svg gave hash 2248379440U not the expected 526339583U 158: file AtropManyChiralsEnhanced.svg gave hash 3480889589U not the expected 348414093U -201: ERROR: [FeaturesValidation] Query atom 0 is not allowed -201: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed -201: ERROR: [FeaturesValidation] Query bond 0 is not allowed -201: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed -201: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed -201: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed -201: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed -201: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed -201: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. -201: here -201: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. -201: there -201: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. 158: file testGithub6968.svg gave hash 1383729159U not the expected 1554428830U -180/230 Test #201: molValidateTest ........................ Passed 0.07 sec -test 202 - Start 202: molChargeTest - -202: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -202: Test timeout computed to be: 1500 -161: [06:21:54] The provided InitialSeed is not an MCS and will be ignored -181/230 Test #197: pyTestPropertyLists ....................***Exception: SegFault 0.27 sec - -test 203 - Start 203: molTautomerTest - -203: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -203: Test timeout computed to be: 1500 -200: [06:21:54] Initializing Normalizer -200: [06:21:54] Running Normalizer -200: [06:21:54] Rule applied: BrokenazidetoN=N+=N- -200: [06:21:54] Initializing Normalizer -200: [06:21:54] Running Normalizer -200: [06:21:54] Initializing Normalizer -200: [06:21:54] Running Normalizer -182/230 Test #200: molNormalizeTest ....................... Passed 0.20 sec -test 204 - Start 204: molStandardizeSmallTest - -204: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -204: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -204: Test timeout computed to be: 1500 -183/230 Test #202: molChargeTest .......................... Passed 0.12 sec -test 205 - Start 205: molFragmentTest - -205: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -205: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -205: Test timeout computed to be: 1500 158: file testGithub7036_2.svg gave hash 1038604245U not the expected 3229829837U 158: file testGithub7036_1.svg gave hash 263989977U not the expected 3059737542U -184/230 Test #198: pyCDXMLTest ............................***Exception: SegFault 0.31 sec - -test 206 - Start 206: molStandardizeCatchTest - -206: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -206: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -206: Test timeout computed to be: 1500 158: file testWedgeNonSingleBonds-1.svg gave hash 1637776400U not the expected 865601717U 158: file testWedgeNonSingleBonds-2.svg gave hash 1102715150U not the expected 2960559495U 158: file testWedgeNonSingleBonds-3.svg gave hash 3275019332U not the expected 1428196589U @@ -32669,61 +32410,30 @@ 158: file testWedgeNonSingleBonds-8.svg gave hash 2146485740U not the expected 3209701539U 158: file testWedgingShouldBeOnSingleBond.svg gave hash 3101383734U not the expected 1002741488U 158: file testDuplicateEnhancedStereoLabelsAddAnnotationFalse.svg gave hash 2694826052U not the expected 2980189527U -185/230 Test #204: molStandardizeSmallTest ................ Passed 0.06 sec -test 207 - Start 207: molStandardizePipelineTest - -207: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -207: Test timeout computed to be: 1500 +161: [02:44:19] The provided InitialSeed is not an MCS and will be ignored 158: file testDuplicateEnhancedStereoLabelsAddAnnotationTrue.svg gave hash 4012232750U not the expected 1462263453U 158: file testComplexQueryAtomMap.svg gave hash 1649284633U not the expected 722421835U 158: file testHighlightHeteroAtoms_1.svg gave hash 2395413774U not the expected 1769258632U 158: file testHighlightHeteroAtoms_2.svg gave hash 3418128330U not the expected 893937335U -207: Randomness seeded to: 2954023293 -207: 1 Counts line too short: '' on line4 -207: 1 Could not instantiate a valid molecule from input -205: [06:21:54] SMARTS Parse Error: syntax error while parsing: [Cl -205: [06:21:54] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -158: file testGithub_7739_1.svg gave hash 1842720796U not the expected 52079325U -186/230 Test #205: molFragmentTest ........................ Passed 0.09 sec -test 208 - Start 208: pyMolStandardize +168/230 Test #177: pyReducedGraphs ........................***Exception: SegFault 0.59 sec -208: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -208: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap -208: Test timeout computed to be: 1500 -207: 8 Molecule has no atoms -207: [06:21:54] Explicit valence for atom # 1 N, 4, is greater than permitted -207: [06:21:54] Explicit valence for atom # 1 N, 4, is greater than permitted -207: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -207: 128 An error occurred while preparing the molecule for standardization. +test 178 + Start 178: trajectoryTest + +178: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Trajectory +178: Test timeout computed to be: 1500 +158: file testGithub_7739_1.svg gave hash 1842720796U not the expected 52079325U +148: processing +148: launch :0 +148: launch :1 +148: launch :2 +148: launch :3 158: file testGithub_7739_2.svg gave hash 492321405U not the expected 2531167697U -207: 8 The molecule contains an unknown isotope: 3C -207: 4 Query atom 0 is not allowed -207: 4 Bond 0 of aromatic type is not allowed -207: 4 Bond 1 of aromatic type is not allowed -207: 4 Bond 2 of aromatic type is not allowed -207: 4 Bond 3 of aromatic type is not allowed -207: 4 Bond 5 of aromatic type is not allowed -207: 4 Bond 6 of aromatic type is not allowed -207: 4 Bond 2 of dative type is not allowed -207: 4 Bond 3 of dative type is not allowed -207: 4 Enhanced stereochemistry features are not allowed -207: 8 The radical at atom 0 is not allowed -207: [06:21:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 158: file testGithub_7739_3.svg gave hash 56331356U not the expected 1126644226U -207: 16 The molecule includes non-null Z coordinates -207: 32 Atom 0 too close to bond 2 -207: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -207: 64 Atom 0 has adjacent stereo bonds with like orientation -207: [06:21:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 158: file testGithub_7739_4.svg gave hash 2285755901U not the expected 9844878U -207: 16 The molecule includes non-null Z coordinates -207: 64 Atom 0 has adjacent stereo bonds with like orientation 158: file testGithub_7739_5.svg gave hash 3374078889U not the expected 2541364166U -158: [06:21:54] +158: [02:44:19] 158: 158: **** 158: Pre-condition Violation @@ -32740,20 +32450,20 @@ 158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x565E03AD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 +158: 8# 0x566743AD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 158: 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -158: 17# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 17# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: -158: [06:21:54] +158: [02:44:19] 158: 158: **** 158: Range Error @@ -32771,20 +32481,20 @@ 158: 6# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 8# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 9# 0x565DF8F6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 16# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 +158: 9# 0x566738F6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 16# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 158: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -158: 18# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 18# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: -158: [06:21:54] +158: [02:44:19] 158: 158: **** 158: Range Error @@ -32802,16 +32512,16 @@ 158: 6# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 7# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 158: 8# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 9# 0x565E04B0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 16# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 +158: 9# 0x566744B0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 16# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 158: 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -158: 18# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 18# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: ---------- 158: **** 158: @@ -32819,9 +32529,8 @@ 158: test cases: 105 | 97 passed | 8 failed 158: assertions: 6801 | 6741 passed | 60 failed 158: -207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -187/230 Test #158: moldraw2DTestCatch .....................***Failed 5.96 sec -Randomness seeded to: 3036021413 +169/230 Test #158: moldraw2DTestCatch .....................***Failed 8.96 sec +Randomness seeded to: 1752506135 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 @@ -32968,36 +32677,36 @@ 4294967295 (0xffffffff) file testGithub3577-1.svg gave hash 1113173858U not the expected 1294276543U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-1.png gave hash 2627351917U not the expected 698316547U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-2.svg gave hash 96083296U not the expected 4132716144U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-2.png gave hash 4101580717U not the expected 1605553248U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-3.svg gave hash 1092525158U not the expected 4199337510U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-3.png gave hash 2781539807U not the expected 2881952238U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-4.svg gave hash 943966498U not the expected 4197407865U -[06:21:49] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:49] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:12] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:12] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-4.png gave hash 1299432584U not the expected 3431655453U file testHandDrawn-5a.svg gave hash 1742606296U not the expected 3628607349U -[06:21:51] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:51] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:15] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:15] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-5b.svg gave hash 2290757626U not the expected 2522138089U -[06:21:51] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -[06:21:51] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +[02:44:15] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +[02:44:15] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-5.png gave hash 1137148752U 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 @@ -33062,7 +32771,7 @@ 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 -[06:21:52] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U +[02:44:16] 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 @@ -33077,7 +32786,7 @@ file testGithub4323_1.png gave hash 1246412143U not the expected 3723958844U file testGithub4323_3.png gave hash 2266718033U not the expected 2185913679U file testGithub4508_1.svg gave hash 3378775316U not the expected 2047652713U -[06:21:52] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +[02:44:17] 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 @@ -33195,7 +32904,7 @@ file acs1996_9.svg gave hash 231896677U not the expected 3747924004U file acs1996_10.svg gave hash 3594677893U not the expected 2229333301U file acs1996_11.svg gave hash 3362983424U not the expected 4107969968U -[06:21:53] 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. +[02:44:18] 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 @@ -33516,7 +33225,7 @@ file testGithub_7739_3.svg gave hash 56331356U not the expected 1126644226U file testGithub_7739_4.svg gave hash 2285755901U not the expected 9844878U file testGithub_7739_5.svg gave hash 3374078889U not the expected 2541364166U -[06:21:54] +[02:44:19] **** Pre-condition Violation @@ -33533,20 +33242,20 @@ 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 - 8# 0x565E03AD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch - 9# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -10# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -11# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -12# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -13# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -14# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -15# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 + 8# 0x566743AD in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch + 9# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +10# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +11# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +12# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +13# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +14# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +15# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 16# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -17# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +17# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch ---------- **** -[06:21:54] +[02:44:19] **** Range Error @@ -33564,20 +33273,20 @@ 6# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 7# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 8# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 - 9# 0x565DF8F6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -10# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -11# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -12# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -13# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -14# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -15# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -16# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 + 9# 0x566738F6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +10# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +11# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +12# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +13# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +14# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +15# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +16# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -18# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +18# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch ---------- **** -[06:21:54] +[02:44:19] **** Range Error @@ -33595,16 +33304,16 @@ 6# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 7# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 8# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu//lib/libRDKitMolDraw2D.so.1 - 9# 0x565E04B0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -10# 0x566C327B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -11# 0x566C3F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -12# 0x566C45C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -13# 0x56693AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -14# 0x56693E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -15# 0x565D90D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -16# 0xF6EE7D43 in /lib/i386-linux-gnu/libc.so.6 + 9# 0x566744B0 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +10# 0x5675727B in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +11# 0x56757F5F in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +12# 0x567585C4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +13# 0x56727AE4 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +14# 0x56727E72 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +15# 0x5666D0D6 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +16# 0xF6F9ED43 in /lib/i386-linux-gnu/libc.so.6 17# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 -18# 0x565D9117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +18# 0x5666D117 in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch ---------- **** @@ -33613,12 +33322,833 @@ assertions: 6801 | 6741 passed | 60 failed -test 209 - Start 209: testScaffoldNetwork +test 179 + Start 179: substructLibraryTest -209: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork -209: Test timeout computed to be: 1500 +179: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary +179: Test timeout computed to be: 1500 +179: [02:44:20] ------------------------------------- +179: [02:44:20] Test1 +144: processing +144: launch :0 +144: launch :1 +144: launch :2 +144: launch :3 +179: [02:44:20] done +179: [02:44:20] ------------------------------------- +179: [02:44:20] Test2 +179: [02:44:21] done +179: [02:44:21] ------------------------------------- +179: [02:44:21] Test3 (stereo options) +170/230 Test #178: trajectoryTest ......................... Passed 1.42 sec +test 180 + Start 180: substructLibraryCatchTest + +180: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary +180: Test timeout computed to be: 1500 +179: [02:44:21] Done (stereo options) +179: [02:44:21] ------------------------------------- +179: [02:44:21] Test4 (trusted smiles) +179: [02:44:21] Done (trusted smiles) +179: [02:44:21] ------------------------------------- +179: [02:44:21] Testing C++ docs +179: [02:44:21] Done (C++ doc tests) +179: [02:44:21] ------------------------------------- +179: [02:44:21] Testing C++ ring query: PatternHolder +179: [02:44:21] Done (C++ ring query tests) +179: [02:44:21] ------------------------------------- +179: [02:44:21] Testing C++ ring query: TautomerPatternHolder +179: [02:44:21] Done (C++ ring query tests) +179: [02:44:21] ------------------------------------- +179: [02:44:21] Add Patterns +180: Randomness seeded to: 1051424845 +180: =============================================================================== +180: All tests passed (171 assertions in 5 test cases) +180: +171/230 Test #180: substructLibraryCatchTest .............. Passed 1.52 sec +test 181 + Start 181: pySubstructLibrary + +181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +181: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +181: Test timeout computed to be: 1500 +172/230 Test #181: pySubstructLibrary .....................***Exception: SegFault 0.90 sec + +test 182 + Start 182: testRGroupDecomp + +182: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +182: Test timeout computed to be: 1500 +182: [02:44:24] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +182: [02:44:24] WARNING: not removing hydrogen atom with dummy atom neighbors +168: Randomness seeded to: 2280990013 +168: Timed out after 11 seconds. +179: [02:44:27] ------------------------------------- +179: [02:44:27] testing PatternHolder +179: [02:44:27] ------------------------------------- +179: [02:44:27] testing TautomerPatternHolder +179: [02:44:27] ------------------------------------- +179: [02:44:27] testSegFaultInHolder +179: [02:44:27] SMILES Parse Error: syntax error while parsing: [02:44:27] [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: syntax error[02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: syntax error while parsing: [02:44:27] [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: dsafsdf[02:44:27] [02:44:27] SMILES[02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [02:44:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [02:44:27] ------------------------------------- +179: [02:44:27] Results do not depend on numThreads +169: Randomness seeded to: 3839555563 +169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +182: iterative +182: bulk +179: [02:44:34] ------------------------------------- +179: [02:44:34] Results do not depend on numThreads (all same) +179: [02:44:35] ------------------------------------- +179: [02:44:35] testTautomerQueries +179: [02:44:35] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +179: [02:44:35] ------------------------------------- +179: [02:44:35] github3881 recursive smarts with rings +173/230 Test #179: substructLibraryTest ................... Passed 15.41 sec +test 183 + Start 183: testRGroupDecompInternals + +183: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +183: Test timeout computed to be: 1500 +182: bulk, no symmetry +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [02:44:35] WARNING: not removing hydrogen atom with dummy atom neighbors +174/230 Test #183: testRGroupDecompInternals .............. Passed 0.21 sec +test 184 + Start 184: rgroupCatchTests + +184: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +184: Test timeout computed to be: 1500 +31: [02:44:35] Finished +31: [02:44:35] ------------------------------------- +31: [02:44:35] Test github1843: RWMol.clear() should not destroy ring pointer. +31: [02:44:35] Finished +31: [02:44:35] ------------------------------------- +31: [02:44:35] Test Github 6370: non-physical radical counts being preserved +31: [02:44:35] Finished +175/230 Test #31: graphmolTest1 .......................... Passed 63.10 sec +test 185 + Start 185: pyRGroupDecomposition + +185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" +185: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap +185: Test timeout computed to be: 1500 +182: [02:44:36] Relabelling existing label +176/230 Test #185: pyRGroupDecomposition ..................***Exception: SegFault 0.80 sec + +test 186 + Start 186: molInterchangeTest1 + +186: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 +186: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange +186: Test timeout computed to be: 1500 +186: [02:44:36] test1: basics +186: [02:44:36] done +186: [02:44:36] test2: basic writing +186: {"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":"2024.09.2","cipRanks":[0,0]}]}]} +186: {"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":"2024.09.2","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} +186: {"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":"2024.09.2","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]]}]}]} +186: {"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":"2024.09.2","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]]}]}]} +186: [02:44:36] done +186: [02:44:36] test3: writing conformers +186: {"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":"2024.09.2","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} +186: [02:44:36] done +186: [02:44:36] test4: writing properties +186: {"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":"2024.09.2","cipRanks":[0,0]}]}]} +186: [02:44:36] done +186: [02:44:36] test5: writing partial charges +186: {"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":"2024.09.2","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[0.5,-0.5]}]}]} +186: [02:44:36] testing parse options +186: [02:44:36] done +186: [02:44:36] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +186: {"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":"2024.09.2","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} +186: [02:44:36] done +186: [02:44:36] testing 'either' stereochemistry +186: [02:44:36] done +177/230 Test #186: molInterchangeTest1 .................... Passed 0.15 sec +test 187 + Start 187: molInterchangeCatchTest + +187: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest +187: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange +187: Test timeout computed to be: 1500 +184: Randomness seeded to: 1210079353 +184: =============================================================================== +184: All tests passed (1475 assertions in 14 test cases) +184: +178/230 Test #184: rgroupCatchTests ....................... Passed 1.26 sec +test 188 + Start 188: pyMolInterchange + +188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" +188: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap +188: Test timeout computed to be: 1500 +187: Randomness seeded to: 3990895266 +187: [02:44:36] unrecognized bond type 12 set to zero while writing +187: [02:44:36] unrecognized bond type 0 set to zero while writing +187: =============================================================================== +187: All tests passed (122 assertions in 6 test cases) +187: +179/230 Test #187: molInterchangeCatchTest ................ Passed 0.18 sec +test 189 + Start 189: testSLNParse + +189: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse/testSLNParse +189: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse +189: Test timeout computed to be: 1500 +189: Atoms: +189: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: +189: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +189: 2 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +189: 3 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +189: 4 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +189: 5 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: +189: Bonds: +189: 0 0->1 order: 1 +189: 1 0->2 order: 1 +189: 2 0->3 order: 1 +189: 3 0->4 order: 1 +189: 4 0->5 order: 1 +189: [02:44:37] SLN Parse Error: syntax error while parsing: CH4[I=13] +189: [02:44:37] Failed parsing SLN 'CH4[I=13]' +189: [02:44:37] SLN Parser error: Atom ID 1 appears *after* its ring closure. +189: [02:44:37] SLN Parser error: Ring closure 1 does not have a corresponding opener. +189: [02:44:37] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +189: [02:44:37] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +189: [02:44:37] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +189: [02:44:37] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +189: [02:44:37] SLN Parse Error: syntax error while parsing: CH4 fff +189: [02:44:37] Failed parsing SLN 'CH4 fff' +189: [02:44:37] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +189: [02:44:37] Failed parsing SLN 'C[charge=+1] foo' +189: [02:44:37] Query property 'is' ignored on non-query atom +189: [02:44:37] Query property 'is' ignored on non-query atom +180/230 Test #189: testSLNParse ........................... Passed 0.21 sec +test 190 + Start 190: pySLNParse + +190: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/Wrap/testSLN.py" +190: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap +190: Test timeout computed to be: 1500 +182: Best mapping +181/230 Test #188: pyMolInterchange .......................***Exception: SegFault 0.76 sec + +test 191 + Start 191: pyGraphMolWrap + +191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rough_test.py" +191: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +191: Test timeout computed to be: 1500 +182/230 Test #182: testRGroupDecomp ....................... Passed 14.11 sec +183/230 Test #190: pySLNParse .............................***Exception: SegFault 0.61 sec + +test 192 + Start 192: pyTestConformerWrap + +192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testConformer.py" +192: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +192: Test timeout computed to be: 1500 +test 193 + Start 193: pyTestTrajectory + +193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testTrajectory.py" +193: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +193: Test timeout computed to be: 1500 +184/230 Test #192: pyTestConformerWrap ....................***Exception: SegFault 0.53 sec + +test 194 + Start 194: pyTestSGroups + +194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testSGroups.py" +194: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +194: Test timeout computed to be: 1500 +185/230 Test #193: pyTestTrajectory .......................***Exception: SegFault 0.80 sec + +test 195 + Start 195: pyTestThreads + +195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testThreads.py" +195: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +195: Test timeout computed to be: 1500 +186/230 Test #191: pyGraphMolWrap .........................***Exception: SegFault 1.26 sec + +test 196 + Start 196: pyTestMultithreadedMolSupplier + +196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +196: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +196: Test timeout computed to be: 1500 +187/230 Test #194: pyTestSGroups ..........................***Exception: SegFault 0.78 sec + +test 197 + Start 197: pyTestPropertyLists + +197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testPropertyLists.py" +197: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 +188/230 Test #195: pyTestThreads ..........................***Exception: SegFault 0.56 sec + +test 198 + Start 198: pyCDXMLTest + +198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/test_cdxml.py" +198: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Wrap +198: Test timeout computed to be: 1500 +189/230 Test #196: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.73 sec + +test 199 + Start 199: molStandardizeTest + +199: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +199: Test timeout computed to be: 1500 +190/230 Test #197: pyTestPropertyLists ....................***Exception: SegFault 0.62 sec + +test 200 + Start 200: molNormalizeTest + +200: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +200: Test timeout computed to be: 1500 +200: [02:44:39] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +200: [02:44:40] Initializing Normalizer +200: [02:44:40] Running Normalizer +200: [02:44:40] Rule applied: BrokenazidetoN=N+=N- +200: [02:44:40] Initializing Normalizer +200: [02:44:40] Running Normalizer +200: [02:44:40] Initializing Normalizer +200: [02:44:40] Running Normalizer +191/230 Test #200: molNormalizeTest ....................... Passed 0.60 sec +test 201 + Start 201: molValidateTest + +201: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +201: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +201: Test timeout computed to be: 1500 +192/230 Test #198: pyCDXMLTest ............................***Exception: SegFault 1.23 sec + +test 202 + Start 202: molChargeTest + +202: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +202: Test timeout computed to be: 1500 +201: ERROR: [FeaturesValidation] Query atom 0 is not allowed +201: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed +201: ERROR: [FeaturesValidation] Query bond 0 is not allowed +201: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed +201: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed +201: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed +201: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed +201: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed +201: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. +201: here +201: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. +201: there +201: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. +193/230 Test #201: molValidateTest ........................ Passed 0.14 sec +test 203 + Start 203: molTautomerTest + +203: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +203: Test timeout computed to be: 1500 +194/230 Test #202: molChargeTest .......................... Passed 0.35 sec +test 204 + Start 204: molStandardizeSmallTest + +204: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +204: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +204: Test timeout computed to be: 1500 +195/230 Test #204: molStandardizeSmallTest ................ Passed 0.15 sec +test 205 + Start 205: molFragmentTest + +205: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +205: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +205: Test timeout computed to be: 1500 +205: [02:44:41] SMARTS Parse Error: syntax error while parsing: [Cl +205: [02:44:41] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +196/230 Test #205: molFragmentTest ........................ Passed 0.19 sec +test 206 + Start 206: molStandardizeCatchTest + +206: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +206: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +206: Test timeout computed to be: 1500 +206: Randomness seeded to: 1587578595 +206: * - * - * - * m1 +206: * - * - * - * m2 +206: * - * - * - * m1 +206: * - * - * - * m2 +206: [02:44:42] Can't kekulize mol. Unkekulized atoms: 3 7 +206: [02:44:42] Can't kekulize mol. Unkekulized atoms: 3 8 +206: [02:44:42] Can't kekulize mol. Unkekulized atoms: 2 3 4 +203: [02:44:43] Tautomer enumeration stopped at 292 tautomers: max transforms reached +197/230 Test #199: molStandardizeTest ..................... Passed 3.92 sec +test 207 + Start 207: molStandardizePipelineTest + +207: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +207: Test timeout computed to be: 1500 +207: Randomness seeded to: 1433983952 +207: 1 Counts line too short: '' on line4 +207: 1 Could not instantiate a valid molecule from input +207: 8 Molecule has no atoms +207: [02:44:43] Explicit valence for atom # 1 N, 4, is greater than permitted +207: [02:44:43] Explicit valence for atom # 1 N, 4, is greater than permitted +207: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +207: 128 An error occurred while preparing the molecule for standardization. +207: 8 The molecule contains an unknown isotope: 3C +207: 4 Query atom 0 is not allowed +207: 4 Bond 0 of aromatic type is not allowed +207: 4 Bond 1 of aromatic type is not allowed +207: 4 Bond 2 of aromatic type is not allowed +207: 4 Bond 3 of aromatic type is not allowed +207: 4 Bond 5 of aromatic type is not allowed +207: 4 Bond 6 of aromatic type is not allowed +207: 4 Bond 2 of dative type is not allowed +207: 4 Bond 3 of dative type is not allowed +207: 4 Enhanced stereochemistry features are not allowed +207: 8 The radical at atom 0 is not allowed +207: [02:44:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: 16 The molecule includes non-null Z coordinates +207: 32 Atom 0 too close to bond 2 +207: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +207: 64 Atom 0 has adjacent stereo bonds with like orientation +207: [02:44:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: 16 The molecule includes non-null Z coordinates +207: 64 Atom 0 has adjacent stereo bonds with like orientation +207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 207: 67108864 The protonation state was adjusted. @@ -33661,28 +34191,58 @@ 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 3 was removed 207: 16777216 The representation of some functional groups was adjusted. -207: [06:21:54] Can't kekulize mol. Unkekulized atoms: 2 3 5 +207: [02:44:44] Can't kekulize mol. Unkekulized atoms: 2 3 5 207: =============================================================================== 207: All tests passed (268 assertions in 5 test cases) 207: -188/230 Test #207: molStandardizePipelineTest ............. Passed 0.26 sec +198/230 Test #207: molStandardizePipelineTest ............. Passed 1.02 sec +test 208 + Start 208: pyMolStandardize + +208: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +208: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap +208: Test timeout computed to be: 1500 +203: [02:44:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached +203: [02:44:44] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +203: [02:44:45] Tautomer enumeration stopped at 25 tautomers: canceled +203: Enumeration was canceled due to timeout (50 ms) +199/230 Test #208: pyMolStandardize .......................***Exception: SegFault 1.01 sec + +test 209 + Start 209: testScaffoldNetwork + +209: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork +209: Test timeout computed to be: 1500 +203: 375 +203: Enumeration has completed +203: [02:44:46] Tautomer enumeration stopped at 40 tautomers: canceled +203: CN=c1cc[nH]cn1 +203: CN=c1ccnc[nH]1 +203: CNc1ccncn1 +203: res: CNc1ccncn1 +203: CN=c1cccc[nH]1 +203: CNc1ccccn1 +203: res: CNc1ccccn1 +200/230 Test #203: molTautomerTest ........................ Passed 8.88 sec test 210 Start 210: pyScaffoldNetwork 210: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 210: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 210: Test timeout computed to be: 1500 -144: validating reference data -115: =>start test GETAWAY custom -115: [06:21:54] test on : 365 molecules done -189/230 Test #115: testRDFcustom .......................... Passed 9.75 sec +209: Randomness seeded to: 2204420698 +209: =============================================================================== +209: All tests passed (269 assertions in 19 test cases) +209: +201/230 Test #209: testScaffoldNetwork .................... Passed 4.39 sec test 211 Start 211: pyScaffoldNetworkPickling 211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 211: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 211: Test timeout computed to be: 1500 -190/230 Test #208: pyMolStandardize .......................***Exception: SegFault 0.31 sec +202/230 Test #210: pyScaffoldNetwork ......................***Exception: SegFault 0.68 sec test 212 Start 212: testMolEnumerator @@ -33690,27 +34250,19 @@ 212: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 212: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator 212: Test timeout computed to be: 1500 -206: Randomness seeded to: 4008055897 -206: * - * - * - * m1 -206: * - * - * - * m2 -206: * - * - * - * m1 -206: * - * - * - * m2 -206: [06:21:54] Can't kekulize mol. Unkekulized atoms: 3 7 -212: Randomness seeded to: 2661603984 -212: [06:21:54] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -206: [06:21:54] Can't kekulize mol. Unkekulized atoms: 3 8 -206: [06:21:54] Can't kekulize mol. Unkekulized atoms: 2 3 4 +212: Randomness seeded to: 4194302204 +212: [02:44:50] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 212: =============================================================================== 212: All tests passed (321 assertions in 16 test cases) 212: -191/230 Test #212: testMolEnumerator ...................... Passed 0.25 sec +203/230 Test #212: testMolEnumerator ...................... Passed 0.32 sec test 213 Start 213: pyMolEnumerator 213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 213: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 213: Test timeout computed to be: 1500 -192/230 Test #210: pyScaffoldNetwork ......................***Exception: SegFault 0.43 sec +204/230 Test #211: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.68 sec test 214 Start 214: testAbbreviations @@ -33718,50 +34270,40 @@ 214: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 214: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations 214: Test timeout computed to be: 1500 -193/230 Test #211: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.39 sec - +214: Randomness seeded to: 599415806 +214: [02:44:50] SMARTS Parse Error: syntax error while parsing: *fail +214: [02:44:50] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +214: [02:44:50] no suitable SubstanceGroups found +214: =============================================================================== +214: All tests passed (195 assertions in 12 test cases) +214: +205/230 Test #214: testAbbreviations ...................... Passed 0.13 sec test 215 Start 215: pyAbbreviations 215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 215: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap 215: Test timeout computed to be: 1500 -214: Randomness seeded to: 405727425 -214: [06:21:55] SMARTS Parse Error: syntax error while parsing: *fail -214: [06:21:55] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -214: [06:21:55] no suitable SubstanceGroups found -214: =============================================================================== -214: All tests passed (195 assertions in 12 test cases) -214: -194/230 Test #214: testAbbreviations ...................... Passed 0.07 sec +206/230 Test #213: pyMolEnumerator ........................***Exception: SegFault 0.63 sec + test 216 Start 216: generalizedSubstructCatch 216: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 216: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct 216: Test timeout computed to be: 1500 -203: [06:21:55] Tautomer enumeration stopped at 292 tautomers: max transforms reached -195/230 Test #213: pyMolEnumerator ........................***Exception: SegFault 0.27 sec - +216: Randomness seeded to: 3382887202 +216: =============================================================================== +216: All tests passed (486 assertions in 10 test cases) +216: +207/230 Test #216: generalizedSubstructCatch .............. Passed 0.51 sec test 217 Start 217: pyGeneralizedSubstruct 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 217: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 217: Test timeout computed to be: 1500 -148: processing -148: launch :0 -148: launch :1 -148: launch :2 -148: launch :3 -123: Warning: Atom Count for residue GLU5A does not match expected count -123: Warning: Atom Count for residue ASN39A does not match expected count -123: Warning: Atom Count for residue GLU53A does not match expected count -123: Warning: Atom Count for residue ARG64A does not match expected count -123: Warning: Atom Count for residue LYS80A does not match expected count -123: Warning: Atom Count for residue GLU150A does not match expected count -123: Warning: Atom Count for residue ASN157A does not match expected count -196/230 Test #215: pyAbbreviations ........................***Exception: SegFault 0.25 sec +208/230 Test #215: pyAbbreviations ........................***Exception: SegFault 0.80 sec test 218 Start 218: testMolProcessing @@ -33769,21 +34311,16 @@ 218: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 218: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing 218: Test timeout computed to be: 1500 -123: =============================================================================== -123: All tests passed (515 assertions in 10 test cases) -123: -197/230 Test #123: descriptorsTestCatch ................... Passed 9.65 sec +209/230 Test #217: pyGeneralizedSubstruct .................***Exception: SegFault 0.55 sec + test 219 Start 219: pyMolProcessing 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 219: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/GraphMol/MolProcessing/Wrap 219: Test timeout computed to be: 1500 -216: Randomness seeded to: 2393266191 -216: =============================================================================== -216: All tests passed (486 assertions in 10 test cases) -216: -198/230 Test #216: generalizedSubstructCatch .............. Passed 0.34 sec +210/230 Test #219: pyMolProcessing ........................***Exception: SegFault 0.46 sec + test 220 Start 220: testQuery @@ -33807,7 +34344,7 @@ 220: XOr 220: pointer and copy foo 220: Set2 -199/230 Test #220: testQuery .............................. Passed 0.01 sec +211/230 Test #220: testQuery .............................. Passed 0.01 sec test 221 Start 221: testMatCalc @@ -33859,87 +34396,68 @@ 221: 9.49496e+07 221: 2.25618e+08 221: 1.30219e+08 -200/230 Test #221: testMatCalc ............................ Passed 0.01 sec +212/230 Test #221: testMatCalc ............................ Passed 0.02 sec test 222 Start 222: pyMatCalc 222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 222: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 222: Test timeout computed to be: 1500 -201/230 Test #217: pyGeneralizedSubstruct .................***Exception: SegFault 0.27 sec - +222: ..... +222: ---------------------------------------------------------------------- +222: Ran 5 tests in 0.807s +222: +222: OK +213/230 Test #222: pyMatCalc .............................. Passed 1.93 sec test 223 Start 223: testSimDivPickers 223: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers/testSimDivPickers 223: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers 223: Test timeout computed to be: 1500 -223: [06:21:55] ------------------------------------- -223: [06:21:55] Testing github issue 1421: MaxMinPicker picking non-existent element. -223: [06:21:55] Done -223: [06:21:55] ------------------------------------- -223: [06:21:55] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -223: [06:21:55] Done -202/230 Test #223: testSimDivPickers ...................... Passed 0.02 sec +223: [02:44:54] ------------------------------------- +223: [02:44:54] Testing github issue 1421: MaxMinPicker picking non-existent element. +223: [02:44:54] Done +223: [02:44:54] ------------------------------------- +223: [02:44:54] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +223: [02:44:54] Done +214/230 Test #223: testSimDivPickers ...................... Passed 0.02 sec test 224 Start 224: pickersTestsCatch 224: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers/pickersTestsCatch 224: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers 224: Test timeout computed to be: 1500 -203/230 Test #199: molStandardizeTest ..................... Passed 1.51 sec +224: Randomness seeded to: 472482434 +224: =============================================================================== +224: All tests passed (21267 assertions in 1 test case) +224: +215/230 Test #224: pickersTestsCatch ...................... Passed 0.17 sec test 225 Start 225: pySimDivPickers 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/testPickers.py" 225: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/SimDivPickers/Wrap 225: Test timeout computed to be: 1500 -204/230 Test #219: pyMolProcessing ........................***Exception: SegFault 0.28 sec - +225: [02:44:55] the useCache argument is deprecated and ignored +225: ...[02:44:55] the useCache argument is deprecated and ignored +225: [02:44:55] the useCache argument is deprecated and ignored +225: .[02:44:55] the useCache argument is deprecated and ignored +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: TOTAL Time elapsed 43.77 seconds +216/230 Test #161: testFMCS ............................... Passed 43.87 sec test 226 Start 226: pyRanker 226: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/testRanker.py" 226: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap 226: Test timeout computed to be: 1500 -182: iterative -224: Randomness seeded to: 3965034056 -224: =============================================================================== -224: All tests passed (21267 assertions in 1 test case) -224: -205/230 Test #224: pickersTestsCatch ...................... Passed 0.15 sec -test 227 - Start 227: testChemicalFeatures - -227: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures -227: Test timeout computed to be: 1500 -227: ----------------------------------------- -227: Test1 -227: Done -206/230 Test #227: testChemicalFeatures ................... Passed 0.01 sec -test 228 - Start 228: pyFeatures - -228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap/testFeatures.py" -228: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap -228: Test timeout computed to be: 1500 -203: [06:21:55] Tautomer enumeration stopped at 292 tautomers: max transforms reached -169: Randomness seeded to: 3216713539 -169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -203: [06:21:55] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -79: =============================================================================== -79: All tests passed (1586 assertions in 98 test cases) -79: -207/230 Test #79: fileParsersCatchTest ................... Passed 12.00 sec -test 229 - Start 229: pythonProjectTests - -229: Test command: /usr/bin/python3 "-m" "pytest" -229: Working Directory: /build/reproducible-path/rdkit-202409.2/Projects -229: Test timeout computed to be: 1500 -225: [06:21:55] the useCache argument is deprecated and ignored -226: ..[06:21:55] +226: ..[02:44:57] 226: 226: **** 226: Invariant Violation @@ -33954,7 +34472,7 @@ 226: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 -226: 6# 0xF58F7637 in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 +226: 6# 0xF5863637 in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 226: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 226: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/rdkit/rdBase.so 226: 9# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 @@ -33964,7 +34482,7 @@ 226: 13# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 226: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/rdkit/rdBase.so 226: 15# boost::python::handle_exception_impl(boost::function0) in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 -226: 16# 0xF58F3E0C in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 +226: 16# 0xF585FE0C in /lib/i386-linux-gnu/libboost_python312.so.1.83.0 226: 17# _PyObject_MakeTpCall in /usr/bin/python3 226: 18# PyObject_Vectorcall in /usr/bin/python3 226: 19# _PyEval_EvalFrameDefault in /usr/bin/python3 @@ -34009,7 +34527,7 @@ 226: 58# Py_RunMain in /usr/bin/python3 226: 59# Py_BytesMain in /usr/bin/python3 226: 60# 0x0815585B in /usr/bin/python3 -226: 61# 0xF7BC7D43 in /lib/i386-linux-gnu/libc.so.6 +226: 61# 0xF7B9ED43 in /lib/i386-linux-gnu/libc.so.6 226: 62# __libc_start_main in /lib/i386-linux-gnu/libc.so.6 226: 63# _start in /usr/bin/python3 226: ---------- @@ -34017,48 +34535,49 @@ 226: 226: ... 226: ---------------------------------------------------------------------- -226: Ran 5 tests in 0.034s +226: Ran 5 tests in 0.065s 226: 226: OK -208/230 Test #226: pyRanker ............................... Passed 0.30 sec +217/230 Test #226: pyRanker ............................... Passed 0.70 sec +test 227 + Start 227: testChemicalFeatures + +227: Test command: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures +227: Test timeout computed to be: 1500 +227: ----------------------------------------- +227: Test1 +227: Done +218/230 Test #227: testChemicalFeatures ................... Passed 0.02 sec +test 228 + Start 228: pyFeatures + +228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap/testFeatures.py" +228: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap +228: Test timeout computed to be: 1500 +219/230 Test #228: pyFeatures .............................***Exception: SegFault 0.36 sec + +test 229 + Start 229: pythonProjectTests + +229: Test command: /usr/bin/python3 "-m" "pytest" +229: Working Directory: /build/reproducible-path/rdkit-202409.2/Projects +229: Test timeout computed to be: 1500 +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 11 tests in 4.356s +225: +225: OK +220/230 Test #225: pySimDivPickers ........................ Passed 4.79 sec test 230 Start 230: pythonSourceTests 230: Test command: /usr/bin/python3 "-m" "pytest" 230: Working Directory: /build/reproducible-path/rdkit-202409.2/rdkit 230: Test timeout computed to be: 1500 -209/230 Test #228: pyFeatures .............................***Exception: SegFault 0.28 sec - -209: Randomness seeded to: 4181986489 -209: =============================================================================== -209: All tests passed (269 assertions in 19 test cases) -209: -210/230 Test #209: testScaffoldNetwork .................... Passed 1.67 sec -203: [06:21:56] Tautomer enumeration stopped at 41 tautomers: canceled -203: Enumeration was canceled due to timeout (50 ms) -222: ..... -222: ---------------------------------------------------------------------- -222: Ran 5 tests in 0.420s -222: -222: OK -211/230 Test #222: pyMatCalc .............................. Passed 0.71 sec -225: ...[06:21:56] the useCache argument is deprecated and ignored -225: [06:21:56] the useCache argument is deprecated and ignored -225: .[06:21:56] the useCache argument is deprecated and ignored -230: ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. -230: __init__.py:6: in -230: from . import rdBase -230: E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) -212/230 Test #230: pythonSourceTests ......................***Failed 0.52 sec -ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. -__init__.py:6: in - from . import rdBase -E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) - -182: bulk 229: Fatal Python error: Segmentation fault 229: -229: Current thread 0xf7b4e700 (most recent call first): +229: Current thread 0xf7f8a700 (most recent call first): 229: File "", line 488 in _call_with_frames_removed 229: File "", line 1289 in create_module 229: File "", line 813 in module_from_spec @@ -34115,10 +34634,10 @@ 229: File "", line 198 in _run_module_as_main 229: 229: Extension modules: rdkit.rdBase, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, rdkit.DataStructs.cDataStructs, rdkit.Chem.rdchem, rdkit.Geometry.rdGeometry, rdkit.Chem.rdinchi, rdkit.Chem.rdCIPLabeler (total: 19) -213/230 Test #229: pythonProjectTests .....................***Exception: SegFault 0.77 sec +221/230 Test #229: pythonProjectTests .....................***Exception: SegFault 1.58 sec Fatal Python error: Segmentation fault -Current thread 0xf7b4e700 (most recent call first): +Current thread 0xf7f8a700 (most recent call first): File "", line 488 in _call_with_frames_removed File "", line 1289 in create_module File "", line 813 in module_from_spec @@ -34176,504 +34695,21 @@ Extension modules: rdkit.rdBase, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, rdkit.DataStructs.cDataStructs, rdkit.Chem.rdchem, rdkit.Geometry.rdGeometry, rdkit.Chem.rdinchi, rdkit.Chem.rdCIPLabeler (total: 19) -203: 375 -203: Enumeration has completed -203: [06:21:57] Tautomer enumeration stopped at 53 tautomers: canceled -144: processing -144: launch :0 -144: launch :1 -144: launch :2 -144: launch :3 -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 11 tests in 1.870s -225: -225: OK -214/230 Test #225: pySimDivPickers ........................ Passed 2.17 sec -179: [06:21:58] ------------------------------------- -179: [06:21:58] testing PatternHolder -203: CN=c1cc[nH]cn1 -203: CN=c1ccnc[nH]1 -203: CNc1ccncn1 -203: res: CNc1ccncn1 -203: CN=c1cccc[nH]1 -203: CNc1ccccn1 -203: res: CNc1ccccn1 -179: [06:21:58] ------------------------------------- -179: [06:21:58] testing TautomerPatternHolder -215/230 Test #203: molTautomerTest ........................ Passed 4.14 sec -179: [06:21:58] ------------------------------------- -179: [06:21:58] testSegFaultInHolder -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf[06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES[06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] [06:21:58] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: [06:21:58] [06:21:58] [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: ' -179: [06:21:58] [06:21:58] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: dsafsdf -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] [06:21:58] [06:21:58] SMILES Parse Error: SMILES Parse Error: [06:21:58] SMILES Parse Error: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] [06:21:58] [06:21:58] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf[06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[06:21:58] SMILES Parse Error: for input: '[06:21:58] [06:21:58] SMILES Parse Error: syntax error while parsing: SMILESSMILES[06:21:58] SMILES Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf' -179: for input: 'syntax error while parsing: dsafsdf -179: [06:21:58] Parse Error: SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf for input: 'Failed parsing SMILES 'dsafsdf'[06:21:58] for input: 'dsafsdf' -179: 'SMILES Parse Error: dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: dsafsdf' -179: syntax error[06:21:58] SMILES Parse Error: ' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] dsafsdf[06:21:58] ' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf -179: for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf[06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf[06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error[06:21:58] [06:21:58] SMILES Parse Error: syntax error[06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: SMILES Parse Error: syntax error while parsing: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: dsafsdf while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [06:21:58] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [06:21:58] ------------------------------------- -179: [06:21:58] Results do not depend on numThreads -93: 0,0 0 -93: 0,1 0 -93: 1,0 0 -93: 1,1 0 -93: 2,0 0 -93: 2,1 0 -216/230 Test #93: testEnumeration ........................ Passed 15.12 sec -182: bulk, no symmetry -218: Randomness seeded to: 77519849 +218: Randomness seeded to: 1395469148 218: =============================================================================== 218: All tests passed (203 assertions in 1 test case) 218: -217/230 Test #218: testMolProcessing ...................... Passed 4.65 sec -182: [06:22:00] Relabelling existing label -182: Best mapping -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -218/230 Test #182: testRGroupDecomp ....................... Passed 8.49 sec -27: All 191 tests passed -168: Randomness seeded to: 2067943749 -168: Timed out after 11 seconds. -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -179: [06:22:02] ------------------------------------- -179: [06:22:02] Results do not depend on numThreads (all same) -179: [06:22:02] ------------------------------------- -179: [06:22:02] testTautomerQueries -179: [06:22:02] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -179: [06:22:02] ------------------------------------- -179: [06:22:02] github3881 recursive smarts with rings -219/230 Test #179: substructLibraryTest ................... Passed 11.22 sec -50: Randomness seeded to: 3827837818 -50: =============================================================================== -50: All tests passed (14835 assertions in 14 test cases) -50: -220/230 Test #50: canonTestsCatch ........................ Passed 21.76 sec -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -27: All 191 tests passed -27: done -27: ------------------------------------- -27: Unit tests for all MMFF constraint terms. -27: 10.0003 -27: done -27: ------------------------------------- -27: Unit test for MMFF TorsionConstraint close to 0 degrees. -27: done -27: ------------------------------------- -27: Unit tests for copying MMFF ForceFields. -27: done -27: ------------------------------------- -27: Unit test for MMFF butane scan. -27: done -221/230 Test #27: testMMFFForceField ..................... Passed 23.80 sec -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: TOTAL Time elapsed 19.39 seconds -222/230 Test #161: testFMCS ............................... Passed 19.48 sec -31: [06:22:08] Finished -31: [06:22:08] ------------------------------------- -31: [06:22:08] Test github1843: RWMol.clear() should not destroy ring pointer. -31: [06:22:08] Finished -31: [06:22:08] ------------------------------------- -31: [06:22:08] Test Github 6370: non-physical radical counts being preserved -31: [06:22:08] Finished -223/230 Test #31: graphmolTest1 .......................... Passed 25.58 sec +222/230 Test #218: testMolProcessing ...................... Passed 8.25 sec +230: ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. +230: __init__.py:6: in +230: from . import rdBase +230: E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) +223/230 Test #230: pythonSourceTests ......................***Failed 1.13 sec +ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. +__init__.py:6: in + from . import rdBase +E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) + 148: --------------------------------- 148: test O3A multithreading bug 148: @@ -34686,42 +34722,39 @@ 148: launch :1 148: launch :2 148: launch :3 -206: [06:22:11] Explicit valence for atom # 0 Br, 1, is greater than permitted +206: [02:45:16] Explicit valence for atom # 0 Br, 1, is greater than permitted 206: =============================================================================== 206: All tests passed (38339 assertions in 50 test cases) 206: -224/230 Test #206: molStandardizeCatchTest ................ Passed 17.51 sec -5: [06:22:17] Finished: testMultipleTimes() -5: [06:22:17] -5: ----------------------------------------- -225/230 Test #5: testConcurrentQueue .................... Passed 33.91 sec +224/230 Test #206: molStandardizeCatchTest ................ Passed 35.27 sec +168: Timed out after 71 seconds. +145: [02:45:36] UFFTYPER: Unrecognized atom type: S_6+6 (0) +145: [02:45:36] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +145: [02:45:36] UFFTYPER: Unrecognized charge state for atom: 0 148: --------------------------------- 148: test getO3AForProbeConfs 148: 148: *********************************************************** -226/230 Test #148: testO3AAlign ........................... Passed 32.49 sec -145: [06:22:23] UFFTYPER: Unrecognized atom type: S_6+6 (0) -145: [06:22:23] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -145: [06:22:23] UFFTYPER: Unrecognized charge state for atom: 0 -144: [06:22:35] done -144: [06:22:35] --------------------------------- -144: [06:22:35] test github issue 256: handling of zero-atom molecules +225/230 Test #148: testO3AAlign ........................... Passed 101.08 sec +144: [02:46:19] done +169: =============================================================================== +169: All tests passed (93 assertions in 5 test cases) +169: +226/230 Test #169: testRascalCluster ...................... Passed 128.32 sec +144: [02:46:19] --------------------------------- +144: [02:46:19] test github issue 256: handling of zero-atom molecules 144: -144: [06:22:35] --------------------------------- -144: [06:22:35] test embedder callback function -144: [06:22:35] --------------------------------- -144: [06:22:35] test multi-threaded multi-conf embedding +144: [02:46:19] --------------------------------- +144: [02:46:19] test embedder callback function +144: [02:46:19] --------------------------------- +144: [02:46:19] test multi-threaded multi-conf embedding 144: -144: [06:22:38] --------------------------------- -144: [06:22:38] test github issue 563: Incorrect ring stereochemistry after embedding +144: [02:46:26] --------------------------------- +144: [02:46:26] test github issue 563: Incorrect ring stereochemistry after embedding 144: 144: CNC[C@H]1CC[C@H](C[NH3+])CC1 -169: =============================================================================== -169: All tests passed (93 assertions in 5 test cases) -169: -227/230 Test #169: testRascalCluster ...................... Passed 50.97 sec -144: [06:22:40] --------------------------------- -144: [06:22:40] test github issue 568: Incorrect stereochemistry after embedding +144: [02:46:30] --------------------------------- +144: [02:46:30] test github issue 568: Incorrect stereochemistry after embedding 144: 144: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 144: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 @@ -34734,7 +34767,11 @@ 144: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 144: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 144: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +145: =============================================================================== +145: All tests passed (12735 assertions in 18 test cases) +145: 144: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +227/230 Test #145: distGeomHelpersCatch ................... Passed 158.21 sec 144: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 144: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 144: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 @@ -34742,10 +34779,10 @@ 144: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 144: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 144: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 -145: =============================================================================== -145: All tests passed (12735 assertions in 18 test cases) -145: -228/230 Test #145: distGeomHelpersCatch ................... Passed 62.79 sec +168: =============================================================================== +168: All tests passed (2923 assertions in 27 test cases) +168: +228/230 Test #168: testRascalMCES ......................... Passed 157.47 sec 144: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 144: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 144: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 @@ -34755,47 +34792,47 @@ 144: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 144: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 144: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -144: [06:23:02] Molecule does not have explicit Hs. Consider calling AddHs() -144: [06:22:57] --------------------------------- -144: [06:22:57] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -144: [06:22:57] --------------------------------- -144: [06:22:57] More ChEMBL molecules failing bounds smoothing. -144: [06:22:57] --------------------------------- -144: [06:22:57] ugly conformations can be generated for highly constrained ring systems. -144: [06:22:57] --------------------------------- -144: [06:22:57] test embed parameters structure. -144: [06:22:57] --------------------------------- -144: [06:22:57] test github 1227: Hs being used in RMSD filtering. -144: [06:22:57] --------------------------------- -144: [06:22:57] Failure to embed larger aromatic rings. -144: [06:22:59] --------------------------------- -144: [06:22:59] Deterministic with large random seeds -144: [06:23:01] --------------------------------- -144: [06:23:01] Github #1990: seg fault after RemoveHs -144: [06:23:01] --------------------------------- -144: [06:23:01] Github #2246: Use coordMap when starting embedding from random coords -144: [06:23:02] --------------------------------- -144: [06:23:02] Providing a distance bounds matrix. -144: [06:23:02] --------------------------------- -144: [06:23:02] Disabling fragmentation. -144: [06:23:02] --------------------------------- -144: [06:23:02] Using symmetry in conformation pruning. -144: [06:23:02] --------------------------------- -144: [06:23:02] Force trans amides. -144: [06:23:02] --------------------------------- -144: [06:23:02] test missing Hs warning. -144: [06:23:02] --------------------------------- -144: [06:23:02] basic H bond support. -144: [06:23:02] ******************************************************* -229/230 Test #144: testDistGeomHelpers .................... Passed 74.91 sec -168: =============================================================================== -168: All tests passed (2923 assertions in 27 test cases) -168: -230/230 Test #168: testRascalMCES ......................... Passed 73.19 sec +5: [02:47:06] Finished: testMultipleTimes() +5: [02:47:06] +5: ----------------------------------------- +229/230 Test #5: testConcurrentQueue .................... Passed 215.04 sec +144: [02:47:15] Molecule does not have explicit Hs. Consider calling AddHs() +144: [02:47:05] --------------------------------- +144: [02:47:05] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +144: [02:47:05] --------------------------------- +144: [02:47:05] More ChEMBL molecules failing bounds smoothing. +144: [02:47:05] --------------------------------- +144: [02:47:05] ugly conformations can be generated for highly constrained ring systems. +144: [02:47:05] --------------------------------- +144: [02:47:05] test embed parameters structure. +144: [02:47:06] --------------------------------- +144: [02:47:06] test github 1227: Hs being used in RMSD filtering. +144: [02:47:06] --------------------------------- +144: [02:47:06] Failure to embed larger aromatic rings. +144: [02:47:09] --------------------------------- +144: [02:47:09] Deterministic with large random seeds +144: [02:47:12] --------------------------------- +144: [02:47:12] Github #1990: seg fault after RemoveHs +144: [02:47:12] --------------------------------- +144: [02:47:12] Github #2246: Use coordMap when starting embedding from random coords +144: [02:47:15] --------------------------------- +144: [02:47:15] Providing a distance bounds matrix. +144: [02:47:15] --------------------------------- +144: [02:47:15] Disabling fragmentation. +144: [02:47:15] --------------------------------- +144: [02:47:15] Using symmetry in conformation pruning. +144: [02:47:15] --------------------------------- +144: [02:47:15] Force trans amides. +144: [02:47:15] --------------------------------- +144: [02:47:15] test missing Hs warning. +144: [02:47:15] --------------------------------- +144: [02:47:15] basic H bond support. +144: [02:47:15] ******************************************************* +230/230 Test #144: testDistGeomHelpers .................... Passed 192.85 sec 74% tests passed, 60 tests failed out of 230 -Total Test time (real) = 79.44 sec +Total Test time (real) = 224.23 sec The following tests FAILED: 2 - pyCoordGen (SEGFAULT) @@ -34861,7 +34898,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' -dh_auto_test: error: cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 returned exit code 2 +dh_auto_test: error: cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 returned exit code 2 make[1]: [debian/rules:149: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' create-stamp debian/debhelper-build-stamp @@ -34871,7 +34908,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_install - cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/rdkit-202409.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/reproducible-path/rdkit-202409.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -34882,61 +34919,91 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/pytest.ini --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/conftest.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbInfo.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbModule.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Stats.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/files.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/StorageUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbConnection.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbResultSet.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbInfo.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWxDc.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/pidTK.py @@ -34944,1189 +35011,1159 @@ -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pidtest.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pstests.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/formatted-strings.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pidtest.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/LazySignature.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/conftest.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__/__init__.cpython-312.pyc +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Sheridan.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Torsions.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Pairs.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Utils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FragmentMatcher.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Matcher.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Generate.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Utils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Utils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/SigFactory.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolCatalog.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/MolSupplier.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/BRICS.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Descriptors3D.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader_sa.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader_orig.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Crippen.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/BulkTester.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PropertyMol.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FragmentCatalog.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasPatcher.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/demoCombined.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/BuilderUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/MolKey.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MACCSkeys.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/IPythonConsole.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/FreeSans.ttf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/SimilarityMaps.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/MolDrawing.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/IPythonConsole.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PropertyMol.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SimpleEnum -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SimpleEnum/Enumerator.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SimpleEnum/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Recap.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MCS.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Lipinski.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SATIS.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/inchi.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/TemplateAlign.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/ShowFeats.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Crippen.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/RegistrationHash.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Graphs.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb --- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fraggle/FraggleSim.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/TorsionFingerprints.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasTools.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/GraphDescriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PyMol.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Subshape/BuilderUtils.py --- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateStereoisomers.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ReducedGraphs.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fraggle/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__init__.py +-- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/github4823.ipynb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState_VSA.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState.py -- Installing: 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Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/InchiInfo.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalFeatures.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolSurf.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SpacialScore.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ReducedGraphs.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Descriptors3D.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/ShowFeats.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FilterCatalog.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Sheridan.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDLogger.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__ --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__/__init__.cpython-312.pyc --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDData.sqlt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/RDKit_Book.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/Install.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example16.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example12.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example17.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example5.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example9.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example15.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/Cookbook.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/exts +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples --- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: 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/build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/MolVS +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/IFG/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/pytest.ini -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__ --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/CreateDb.cpython-312.pyc -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/CreateDb.cpython-312.pyc +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/test.sh +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/README.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/README.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2024.09.2 @@ -36169,12 +36206,12 @@ -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/test.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2024.09.2 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -36762,12 +36799,15 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' 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 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 Clustering.so to Clustering.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 rdInfoTheory.so to rdInfoTheory.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 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 cDataStructs.so to cDataStructs.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 rdForceField.so to rdForceField.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 rdGeometry.so to rdGeometry.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 @@ -36807,13 +36847,10 @@ I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-312-i386-linux-gnu.so 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 rdMolStandardize.so to rdMolStandardize.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 rdScaffoldNetwork.so to rdScaffoldNetwork.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 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 +I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-i386-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_installsystemduser -O--buildsystem=cmake @@ -37435,48 +37472,48 @@ diversion by libc6 from: /lib/ld-linux.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux.so.2.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol MemoryContextAllocZero: it's probably a plugin +dpkg-shlibdeps: warning: diversions involved - output may be incorrect + diversion by libc6 from: /lib/ld-linux.so.2 +dpkg-shlibdeps: warning: diversions involved - output may be incorrect + diversion by libc6 to: /lib/ld-linux.so.2.usr-is-merged +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol MemoryContextAlloc: it's probably a plugin dpkg-shlibdeps: warning: 25 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 from: /lib/ld-linux.so.2 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - 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: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: 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: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} 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 rdkit-data: 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: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-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 dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_i386.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.2-2_i386.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.2-2_all.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_i386.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.2-2_all.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_i386.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.2-2_i386.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_i386.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.2-2_i386.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_i386.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.2-2_i386.deb'. +dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_i386.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.2-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.2-2_i386.buildinfo dpkg-genchanges --build=binary -O../rdkit_202409.2-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37484,12 +37521,14 @@ 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/22658/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22658/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/104417 and its subdirectories -I: Current time: Thu Jan 1 06:25:12 -12 2026 -I: pbuilder-time-stamp: 1767291912 +I: removing directory /srv/workspace/pbuilder/22658 and its subdirectories +I: Current time: Sat Nov 30 02:52:02 +14 2024 +I: pbuilder-time-stamp: 1732884722