Diff of the two buildlogs: -- --- b1/build.log 2024-12-17 21:19:43.276948642 +0000 +++ b2/build.log 2024-12-17 21:36:25.423532457 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 17 08:39:23 -12 2024 -I: pbuilder-time-stamp: 1734467963 +I: Current time: Tue Jan 20 17:42:47 +14 2026 +I: pbuilder-time-stamp: 1768880567 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ 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/3972870/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2227627/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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 Jan 20 03:43 /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/2227627/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2227627/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a35516a897534845bccdbd33d9b729ca' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3972870' - PS1='# ' - PS2='> ' + INVOCATION_ID=be2cadd2abb34833bae0afb7ce2706ab + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2227627 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.wWec19YJ/pbuilderrc_2WxU --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.wWec19YJ/b1 --logfile b1/build.log rdkit_202409.2-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wWec19YJ/pbuilderrc_Xdei --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.wWec19YJ/b2 --logfile b2/build.log rdkit_202409.2-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 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 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3972870/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2227627/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -569,7 +601,7 @@ Get: 367 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] -Fetched 418 MB in 6s (74.0 MB/s) +Fetched 418 MB in 22s (19.0 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 ... 19966 files and directories currently installed.) @@ -1757,8 +1789,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 17 20:44:08 UTC 2024. -Universal Time is now: Tue Dec 17 20:44:08 UTC 2024. +Local time is now: Tue Jan 20 03:45:12 UTC 2026. +Universal Time is now: Tue Jan 20 03:45:12 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4) ... @@ -2145,7 +2177,11 @@ 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/2227627/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2227627/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 @@ -2251,7 +2287,7 @@ -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (3.1s) +-- Configuring done (4.4s) -- Generating done (1.9s) CMake Warning: Manually-specified variables were not used by the project: @@ -2286,14 +2322,14 @@ -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/x86_64-linux-gnu/libpq.so (found version "17.2") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (1.0s) +-- Configuring done (2.1s) -- 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-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2303,18 +2339,18 @@ make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/GA /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/GA /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -2325,82 +2361,82 @@ cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDStreams/streams.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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/usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hcdriver.c +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/catch_main.cpp +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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 -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/GA/ga/Chromosome.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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%] Built target inchi_support -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /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 -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2024.09.2 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2024.09.2 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 1%] Built target hc -[ 2%] Linking CXX shared library ../../lib/libRDKitga.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -[ 2%] Linking CXX static library librdkitCatch.a +[ 1%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +[ 2%] Linking CXX shared library ../../lib/libRDKitga.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.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-x86_64-linux-gnu' @@ -2428,21 +2464,21 @@ make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.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-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make 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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/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 @@ -2450,8 +2486,8 @@ cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral 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Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -2465,126 +2501,116 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/testRDValue.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-x86_64-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_64BIT_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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/build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogParams.cpp -[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Built target testConcurrentQueue +[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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../../../lib/libRDKitEigenSolvers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 5%] Built target EigenSolvers -[ 5%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 [ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 5%] Built target logTestsCatch +[ 5%] Built target EigenSolvers /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 5%] Built target Catalogs -[ 5%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 [ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 5%] Built target testMatrices +[ 5%] Built target Catalogs /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../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-x86_64-linux-gnu' @@ -2597,8 +2623,20 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 5%] Built target logTestsCatch +[ 5%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 5%] Built target testMatrices [ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +[ 6%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' @@ -2607,254 +2645,285 @@ make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -[ 9%] Built target testRDValue -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ML/Data /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testDict.dir/link.d CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 9%] Built target testDict make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 9%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Data/cQuantize.cpp [ 9%] Built target RDGeometryLib 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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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9%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 9%] Built target pickersTestsCatch make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && 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Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/AlignPoints.cpp -[ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 9%] Built target Clustering -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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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 -[ 9%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -[ 9%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 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"--color=" +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 11%] Built target pickersTestsCatch +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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{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>, @@ -3115,207 +3184,174 @@ /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 shared library ../../../lib/libRDKitAlignment.so -cd 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -[ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -make[4]: Leaving 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executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Aromaticity.cpp -[ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -[ 14%] Built target rdAlignment -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security 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/usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/rdAlignment.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 16%] Built target rdGeometry [ 16%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3331,439 +3367,457 @@ make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/Trajectory.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmartsWrite.cpp -[ 21%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversions.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so -[ 23%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 23%] Built target GenericGroups +[ 27%] Built target MolTransforms make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend -[ 23%] Building CXX object 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 27%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script 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../../../../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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 24%] Built target rdBase -[ 24%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /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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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 24%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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-c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +[ 27%] Built target testOptimizer +[ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-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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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 27%] Built target rdtrajectory +[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 24%] Built target ShapeHelpers +[ 27%] Built target ShapeHelpers 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/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 -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/PositionConstraint.cpp -[ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -[ 24%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +[ 27%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -[ 24%] Built target rdqueries -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/TorsionConstraint.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so +[ 27%] Built target rdCIPLabeler +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' +[ 27%] Built target ForceField +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Params.cpp -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Nonbonded.cpp -[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/Params.cpp +[ 28%] Built target rdSLNParse [ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -[ 28%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' @@ -3778,21 +3832,22 @@ make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -3801,527 +3856,468 @@ cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make 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directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -[ 30%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 31%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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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 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +[ 32%] Built target graphmolIterTest [ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD 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-o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 32%] Built target MolAlign -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make[4]: Entering directory 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-cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp -[ 34%] Built target rdCIPLabeler -make -f 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 35%] Built target moliteratorTestsCatch +[ 35%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2024.09.2 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CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/test1.cpp +[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -cd 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl [ 35%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 35%] Built target MolChemicalFeatures -[ 35%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 -[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2024.09.2 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2024.09.2 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 35%] Built target Abbreviations -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -make[4]: 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/ForceField.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 36%] Built target rdReducedGraphs -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu 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CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp +[ 35%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 36%] Built target ForceFieldsCatch -[ 36%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD 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/usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 35%] Built target MolChemicalFeatures +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 36%] Built target rdAbbreviations -[ 37%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +[ 37%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 37%] Built target testReducedGraphs /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -4342,12 +4338,53 @@ cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 38%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 38%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +[ 38%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 38%] Built target graphmolqueryTest +[ 38%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 38%] Built target FilterCatalog +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 38%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +[ 39%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 39%] Built target rdReducedGraphs +[ 39%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 39%] Built target testSLNParse +[ 39%] Linking CXX executable forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 39%] Built target forceFieldHelpersCatch +[ 39%] Linking CXX executable ForceFieldsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../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 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 39%] Built target ForceFieldsCatch +[ 39%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../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 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 38%] Built target DistGeometry +[ 39%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend @@ -4358,106 +4395,105 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 38%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -[ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/DistGeom.cpp -[ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -[ 38%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 39%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +[ 39%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +[ 39%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +[ 39%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +[ 39%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/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 -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 39%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat 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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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 39%] Built target FilterCatalog -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +[ 40%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.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 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 40%] Built target testDistGeom [ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 40%] Built target rdForceFieldHelpers -[ 40%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.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 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 40%] Built target testDistGeom [ 40%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 40%] Built target rdForceField [ 40%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 40%] Built target rdForceField [ 40%] Built target DistGeom [ 40%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 @@ -4478,9 +4514,14 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 41%] Built target DistGeomHelpers +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../../../../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/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 41%] Built target rdMHFPFingerprint [ 41%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 -[ 41%] Built target DistGeomHelpers /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' @@ -4493,11 +4534,21 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.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/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 42%] Built target rdFingerprintGenerator /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 42%] Built target rdDepictor +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 42%] Built target rdMolHash [ 42%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4510,88 +4561,73 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' +[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.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/Mol2FileParser.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/CDXMLParser.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SequenceWriters.cpp -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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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/rdinchi.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 45%] Built target rdinchi [ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4610,506 +4646,392 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" 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[4]: Entering 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"--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu 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+make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend +make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make 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Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" +make[4]: Entering directory 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directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 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+cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" +cd 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make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 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Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu 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Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 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Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target pickleTestsCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 testUFFForceField -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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%] Linking CXX executable graphmolAdjustQueryCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target graphmolAdjustQueryCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu 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&& /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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/build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/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 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Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 50%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 graphmolTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target graphmolTest1 -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target testMMFFForceField -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 50%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libcoordgen.so 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 50%] Linking CXX executable testGeneralFileReader -[ 50%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -[ 50%] Built target testGeneralFileReader -make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 50%] Built target testMultithreadedMolSupplier -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o +[ 47%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o +[ 47%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +[ 47%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o +[ 47%] Building CXX object 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target testDepictor -make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend -make[4]: Entering directory 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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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +[ 50%] Linking CXX executable test-valgrind +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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 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../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target graphmoltestPickler +[ 50%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +[ 50%] Built target testExtendedStereoParsing +[ 50%] Built target test-valgrind make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -[ 50%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target testTplParser -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target testExtendedStereoParsing +[ 50%] Built target testMol2ToMol 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 50%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable testSquiggleDoubleBonds +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 50%] Built target graphmoltestChirality +[ 50%] Built target testSquiggleDoubleBonds 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" @@ -5118,11 +5040,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 51%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 51%] Built target connectTheDotsTest +[ 51%] Built target testTplParser make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" @@ -5131,44 +5053,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/catch_tests.cpp -/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)}) { - | ^ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-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)}) { - | ^ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-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)}) { - | ^ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-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)}) { - | ^ -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-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)}) { - | ^ -/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)}) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 51%] Linking CXX executable v2FileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 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-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 [ 51%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -[ 51%] Linking CXX executable v2MolSuppliers -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +[ 51%] Linking CXX executable testMultithreadedMolSupplier /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-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 [ 51%] Built target XYZFileParserCatchTest +[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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/usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 51%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" +[ 51%] Linking CXX executable molBundleTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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/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 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable graphmolOrganometallicsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 51%] Built target v2MolSuppliers +[ 51%] Built target molBundleTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -5203,63 +5103,122 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 51%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -[ 52%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 52%] Built target testMolWriter +[ 51%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +[ 51%] Built target graphmolOrganometallicsCatch make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend -[ 52%] Built target multithreadedSupplierCatchTest +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" +[ 51%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 51%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 +[ 51%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 51%] Built target resMolSupplierTest +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 51%] Built target testGeneralFileReader make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 -[ 52%] Built target testMolSupplier +[ 51%] Linking CXX executable pickleTestsCatch +[ 51%] Built target connectTheDotsTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 make[4]: Entering directory 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-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o +[ 51%] Built target graphmoltestPicklerGlobalSetting +[ 51%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o 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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 52%] Built target molfileStereoCatchTest +[ 52%] Built target testUFFForceField +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 52%] Built target pickleTestsCatch +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/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)}) { + | ^ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' + 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-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)}) { + | ^ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' + 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-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)}) { + | ^ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-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)}) { + | ^ +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-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)}) { + | ^ +/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)}) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 52%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 52%] Built target hanoiTest +[ 52%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" @@ -5268,41 +5227,63 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection 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Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 52%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5311,11 +5292,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 53%] Built target testMHFPFingerprint +[ 53%] Built target v2MolSuppliers make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" @@ -5324,134 +5305,132 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/test1.cpp -[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Built target filterCatalogTest +[ 53%] Built target multithreadedSupplierCatchTest make -f Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o +[ 53%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/catch_tests.cpp -[ 54%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Built target graphmolTestsCatch +[ 53%] Built target testPropertyLists make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 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Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat 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Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 53%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Built target substructTestCatch +[ 54%] Built target testMolWriter make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Linking CXX executable testSubstructMatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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=. 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 56%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 55%] Built target testFragCatalog +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 +[ 56%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 56%] Built target testMMFFForceFieldHelpersMultiThread +[ 56%] Built target filterCatalogTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" @@ -5460,18 +5439,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ 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Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/catch_tests.cpp -[ 56%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -[ 56%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -[ 56%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -[ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../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 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 57%] Built target testCrystalForceField make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +[ 57%] Linking CXX executable molTransformsTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -5479,395 +5449,376 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/x86_64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../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/x86_64-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 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 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cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/PMI.cpp +[ 61%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +[ 61%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 61%] Built target testUFFForceFieldHelpers -[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.cpp -[ 61%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 64%] Built target testUFFForceFieldHelpers +[ 64%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 61%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -[ 61%] Built target testFingerprints -[ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 61%] Linking CXX executable trajectoryTest +[ 64%] Built target smiTest1 +[ 64%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.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 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 64%] Built target rdDistGeom +[ 64%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -[ 61%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 61%] Built target trajectoryTest -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 62%] Built target rdDistGeom -[ 62%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 62%] Built target MMPA +[ 65%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 62%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 62%] Built target molHashCatchTest -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +[ 65%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 62%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -[ 63%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 65%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 65%] Built target smiTestCatch +[ 65%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 63%] Built target molInterchangeCatchTest +[ 65%] Built target testFingerprints +[ 66%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 63%] Built target MolProcessing +[ 66%] Built target MolProcessing make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend +make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/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 -[ 63%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build +make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 66%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o +[ 66%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 63%] Built target molInterchangeTest1 -[ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 63%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 67%] Built target rdMolProcessing -[ 67%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 67%] Built target FMCS -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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/Test /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +[ 67%] Built target testDistGeomHelpers +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 67%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +[ 67%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 [ 67%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +[ 67%] Built target molHashCatchTest +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 ../../../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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 67%] Built target molInterchangeCatchTest /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' @@ -5876,774 +5827,1094 @@ make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" 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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" -make[4]: Entering directory 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Leaving directory 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testReaction.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 68%] Built target Deprotect -[ 69%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 -[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 69%] Built target RascalMCES +[ 70%] Built target Deprotect +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextJS.cpp make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" -[ 69%] Linking CXX executable testReactionFingerprints make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -[ 69%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +[ 71%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/deprotectTest.cpp +[ 72%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT 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../../../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-x86_64-linux-gnu' +[ 73%] Built target RascalMCES +[ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD 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/usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 73%] Built target rdMolProcessing +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 73%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ChiralityOps.cpp +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 69%] Built target testReactionFingerprints +[ 73%] Built target testReactionFingerprints +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 73%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 73%] Built target fileParsersTest1 +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd 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Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/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_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 69%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp +[ 73%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/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_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +[ 73%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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../../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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 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../../../lib/libRDKitPartialCharges.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/x86_64-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 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' +[ 75%] Built target Descriptors +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend +make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 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+cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp -[ 71%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 71%] Built target MarvinParser -make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testMORSE.cpp -[ 73%] Linking CXX executable testBCUT -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 +[ 80%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +[ 80%] Linking CXX shared module 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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/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/rxn_test1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 78%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -[ 78%] Built target test3D -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +[ 80%] Built target rdDeprotect +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 79%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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../../../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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 80%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/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_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT 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CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +[ 80%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +[ 80%] Linking CXX executable testFMCS +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' +[ 80%] Built target MarvinParser +[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 80%] Built target testFMCS +[ 80%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 80%] Built target testCoulombMat +[ 80%] Built target rdMolEnumerator 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 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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 -[ 81%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 81%] Linking CXX executable descriptorsTestCatch -cd 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molValidateTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +[ 84%] Built target molFragmentTest +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 84%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +[ 84%] Built target molValidateTest +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 84%] Built target molChargeTest +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +[ 85%] Built target test3D +[ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 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/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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/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 +[ 85%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 81%] Built target O3AAlign -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend -make[4]: Entering directory 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Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 -[ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 82%] Built target rdMolEnumerator -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +[ 85%] Built target descriptorsTestCatch +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 85%] Linking CXX executable molStandardizeTest +[ 86%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +[ 86%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 86%] Built target molStandardizeTest +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 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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/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testCharge.cpp -[ 83%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -[ 83%] Linking CXX executable testMrvToMol -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 +[ 86%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 83%] Built target TautomerQuery -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so +[ 86%] Built target TautomerQuery +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 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'/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 83%] Built target molStandardizeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend +[ 88%] Built target molStandardizePipelineTest +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 90%] Built target testDescriptors +[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTWriter.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, @@ -6672,17 +6943,11 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 84%] Built target molValidateTest -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp +[ 90%] Built target cxsmilesTest +[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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] @@ -6702,306 +6967,76 @@ /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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 84%] Built target testMolEnumerator -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 -[ 85%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 91%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 +[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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../../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp -[ 91%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/molStandardizeCatchTest.dir/link.d CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a 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CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 -[ 92%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -[ 92%] Linking CXX executable moldraw2DRxnTest1 -cd 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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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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 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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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 92%] Built target rdmolfiles -[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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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 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so +[ 94%] Built target rdMolStandardize +[ 94%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +[ 94%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp -[ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 93%] Linking CXX executable testCIPLabeler -cd 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 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../../../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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7009,82 +7044,73 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 94%] Built target GeneralizedSubstruct make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend +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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 94%] Linking CXX shared module 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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd 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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o [ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o +cd 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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 +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/PatternFactory.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o +[ 96%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-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_64BIT_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 96%] Built target rdMolDescriptors [ 96%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 96%] Built target moldraw2DTest1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 96%] Built target rdChemReactions /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, @@ -7095,16 +7121,6 @@ /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/adapter.cpp:1618:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1618 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ -[ 96%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 96%] Built target rdchem -[ 96%] Linking CXX executable generalizedSubstructCatch -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 96%] Built target generalizedSubstructCatch [ 96%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7118,72 +7134,92 @@ [ 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[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" +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-x86_64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/depend cd 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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%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 96%] Built target rdmolfiles [ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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library librdkit.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/PgSQL/rdkit/sql cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/PgSQL/rdkit/data +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/expected 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 96%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 [ 96%] Built target rdkit -[ 96%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 96%] Built target testReaction +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 96%] Built target rdChemReactions +[ 96%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 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../../../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/x86_64-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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 96%] Built target gaExample +[ 96%] Built target rdchem [ 97%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [ 97%] Built target testRGroupDecompInternals +[ 97%] Linking CXX executable gaExample +cd 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../../../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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +[ 97%] Built target gaExample [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so @@ -7200,22 +7236,22 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +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-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o [ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-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/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7233,11 +7269,11 @@ [100%] Built target moldraw2DTestCatch [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 -[100%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target substructLibraryCatchTest +[100%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../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/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/x86_64-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/x86_64-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/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/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' [100%] Built target substructLibraryTest @@ -7380,74 +7416,74 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol -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/MolTransforms 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/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations -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/SubstructLibrary -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/MolInterchange -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/Trajectory +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/RGroupDecomposition 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/ScaffoldNetwork -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/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints 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/MolEnumerator -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct 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/MolChemicalFeatures +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/SubstructLibrary +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/MarvinParse +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations +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/libs 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/MolHash +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/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/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints -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/PartialCharges +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/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/UFF +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/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct +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/FileParsers +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/MolStandardize +Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/FragmentCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/AcidBaseCatalog -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/RGroupDecomposition -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/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/DistGeomHelpers +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/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/MolChemicalFeatures -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/MolDraw2D +Searching 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/MolDraw2D/Qt Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Qt/Demo -Searching 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/PartialCharges -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/GraphMol/StructChecker -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/ChemTransforms -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse +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/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers -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/ChemReactions +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/ChemReactions/Enumerate +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/SLNParse +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/GraphMol/MolEnumerator +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/GenericGroups 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/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/InfoTheory 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 Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers @@ -7460,8 +7496,8 @@ 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/ForceField/MMFF 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/Optimizer +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/Geometry Searching for files in directory /build/reproducible-path/rdkit-202409.2/Code/Features @@ -8457,9 +8493,6 @@ Generating code for file ForceField.h... Generating code for file OopBend.h... Generating code for file StretchBend.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... @@ -8483,6 +8516,9 @@ Generating code for file PositionConstraint.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... @@ -8580,6 +8616,8 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -8698,8 +8736,6 @@ Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -8716,8 +8752,6 @@ 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... @@ -8779,6 +8813,8 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... +Generating code for file Tautomer.h... +Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -8891,9 +8927,6 @@ Generating docs for file ForceField.h... Generating docs for file OopBend.h... Generating docs for file StretchBend.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... @@ -8917,6 +8950,9 @@ Generating docs for file PositionConstraint.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... Generating docs for file Utils.h... Generating docs for file Utils.h... Generating docs for file Grid3D.h... @@ -9014,6 +9050,8 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -9118,11 +9156,11 @@ Generating docs for file MolDraw2D.h... Generating docs for file MolDraw2DCairo.h... Generating docs for file MolDraw2DDetails.h... -Generating docs for file MolDraw2DHelpers.h... -Generating docs for file MolDraw2DJS.h... -Gener/build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' +Generating docs fo/build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202409.2/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' -ating docs for file MolDraw2DSVG.h... +r file MolDraw2DHelpers.h... +Generating docs for file MolDraw2DJS.h... +Generating docs for file MolDraw2DSVG.h... Generating docs for file MolDraw2DUtils.h... Generating docs for file MolDraw2Dwx.h... Generating docs for file DrawTextFTQt.h... @@ -9134,8 +9172,6 @@ Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -9152,8 +9188,6 @@ 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... @@ -9215,6 +9249,8 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... +Generating docs for file Tautomer.h... +Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -11238,9 +11274,9 @@ copying downloadable files... [100%] C++Examples/example16.cpp copying static files... -Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/language_data.js -Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/documentation_options.js +Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... @@ -12520,8 +12556,8 @@ copying assets... copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/make.bat Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/latexmkrc Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/latexmkjarc +Writing evaluated template result to /build/reproducible-path/rdkit-202409.2/Docs/Book/_build/latex/latexmkrc done copying assets: done processing RDKit.tex... @@ -12786,7 +12822,7 @@ 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)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -15763,10 +15799,10 @@ find /build/reproducible-path/rdkit-202409.2 -name rdchem.so /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j20 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -15899,10 +15935,142 @@ 20: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/testMatrices 20: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 -1: core -1: RDKit 2D -1: -1: 4 4 0 0 0 0 0 0 0 0999 V2000 +test 21 + Start 21: testConrec + +21: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/testConrec +21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment +22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment +22: Test timeout computed to be: 1500 +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-x86_64-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-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch +25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField +26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/Code/DistGeom/testDistGeom +29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest +32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +test 33 + Start 33: graphmolqueryTest + +33: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +33: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 +test 35 + Start 35: graphmoltestChirality + +35: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality +35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +test 36 + Start 36: graphmoltestPickler + +36: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler +36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +test 37 + Start 37: graphmoltestPicklerGlobalSetting + +37: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +test 38 + Start 38: graphmolIterTest + +38: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest +38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +test 39 + Start 39: hanoiTest + +39: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest +39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +test 40 + Start 40: graphmolMemTest1 + +40: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 +test 41 + Start 41: resMolSupplierTest + +41: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +test 42 + Start 42: molBundleTest + +42: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest +42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +1: core +1: RDKit 2D +1: +1: 4 4 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 @@ -16356,8 +16524,8 @@ 1: 2 5 1 0 1: M END 1: -3: [09:08:12] Testing Github940: property dictionaries leaking memory -3: [09:08:12] done +3: [17:54:59] Testing Github940: property dictionaries leaking memory +3: [17:54:59] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect @@ -16374,48 +16542,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [09:08:12] +5: [17:54:59] 5: ----------------------------------------- -5: [09:08:12] Finished: testPushAndPop() -5: [09:08:12] +5: [17:54:59] Finished: testPushAndPop() +5: [17:54:59] 5: ----------------------------------------- -5: [09:08:12] +5: [17:54:59] 5: ----------------------------------------- -6: Randomness seeded to: 2222902983 +6: Randomness seeded to: 2405775674 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: Randomness seeded to: 128778159 -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent -7: [09:08:12] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: Randomness seeded to: 1551853224 +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent +7: [17:54:59] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [09:08:12] pass -8: [09:08:12] v3 4 -8: [09:08:12] v4 5 -8: [09:08:12] SPARSE ----------------------------------- -8: [09:08:12] Set 10: 0 -8: [09:08:12] Set 11: 0 -8: [09:08:12] Set 14: 0 -8: [09:08:12] Set 10: 1 -8: [09:08:12] Get 14: 1 -8: [09:08:12] Num: 20 -8: [09:08:12] NumOn: 3 -8: [09:08:12] NumOff: 17 +8: [17:54:59] pass +8: [17:54:59] v3 4 +8: [17:54:59] v4 5 +8: [17:54:59] SPARSE ----------------------------------- +8: [17:54:59] Set 10: 0 +8: [17:54:59] Set 11: 0 +8: [17:54:59] Set 14: 0 +8: [17:54:59] Set 10: 1 +8: [17:54:59] Get 14: 1 +8: [17:54:59] Num: 20 +8: [17:54:59] NumOn: 3 +8: [17:54:59] NumOff: 17 8: 10, 11, 14, -8: [09:08:12] t2[19]: 0 -8: [09:08:12] t2[14]: 1 -8: [09:08:12] t2[19]: 0 -8: [09:08:12] t2[14]: 0 +8: [17:54:59] t2[19]: 0 +8: [17:54:59] t2[14]: 1 +8: [17:54:59] t2[19]: 0 +8: [17:54:59] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16423,20 +16591,20 @@ 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: [09:08:12] Explicit ---------------------------------- -8: [09:08:12] Set 10: 0 -8: [09:08:12] Set 11: 0 -8: [09:08:12] Set 14: 0 -8: [09:08:12] Set 10: 1 -8: [09:08:12] Get 14: 1 -8: [09:08:12] Num: 20 -8: [09:08:12] NumOn: 3 -8: [09:08:12] NumOff: 17 +8: [17:54:59] Explicit ---------------------------------- +8: [17:54:59] Set 10: 0 +8: [17:54:59] Set 11: 0 +8: [17:54:59] Set 14: 0 +8: [17:54:59] Set 10: 1 +8: [17:54:59] Get 14: 1 +8: [17:54:59] Num: 20 +8: [17:54:59] NumOn: 3 +8: [17:54:59] NumOff: 17 8: 10, 11, 14, -8: [09:08:12] t2[19]: 0 -8: [09:08:12] t2[14]: 1 -8: [09:08:12] t2[19]: 0 -8: [09:08:12] t2[14]: 0 +8: [17:54:59] t2[19]: 0 +8: [17:54:59] t2[14]: 1 +8: [17:54:59] t2[19]: 0 +8: [17:54:59] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16444,30 +16612,30 @@ 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: [09:08:12] Done -8: [09:08:12] Test DiscreteValue Vectors 1 ---------------------------- -8: [09:08:12] Expected failure: Value out of range -8: [09:08:12] Expected failure: Value out of range -8: [09:08:12] Expected failure: Value out of range -8: [09:08:12] Expected failure: Value out of range -8: [09:08:12] Expected failure: Value out of range -8: [09:08:12] Test DiscreteValue Vectors 2 ------------------------------ -8: [09:08:12] Test DiscreteValue Vectors 3 --------------------------- -8: [09:08:12] Test DiscreteValue Operations ----------------------------- -8: [09:08:12] Test DiscreteValue Operations 2 -------------------------- -8: [09:08:12] Test SparseIntVect ------------------------------------ -8: [09:08:12] Test SparseIntVect Serialization -------------------------- -8: [09:08:12] Test BitVect Serialization ------------------------------- -8: [09:08:12] Test BitVect to FPS ------------------------------- -8: [09:08:12] Test BitVect to binary string ------------------------------- -8: [09:08:12] Test Similarity Measures BitVect ------------------------------- -8: [09:08:12] Test Similarity Measures SparseBitVect ------------------------------- -8: [09:08:12] Test BitVect with all ones ------------------------------- -8: [09:08:12] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [09:08:12] Test bitmap operations ------------------------------- -8: [09:08:12] Test bitmaps as properties ------------------------------- -8: [09:08:12] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -11: Randomness seeded to: 2532056721 +8: [17:54:59] Done +8: [17:54:59] Test DiscreteValue Vectors 1 ---------------------------- +8: [17:54:59] Expected failure: Value out of range +8: [17:54:59] Expected failure: Value out of range +8: [17:54:59] Expected failure: Value out of range +8: [17:54:59] Expected failure: Value out of range +8: [17:54:59] Expected failure: Value out of range +8: [17:54:59] Test DiscreteValue Vectors 2 ------------------------------ +8: [17:54:59] Test DiscreteValue Vectors 3 --------------------------- +8: [17:54:59] Test DiscreteValue Operations ----------------------------- +8: [17:54:59] Test DiscreteValue Operations 2 -------------------------- +8: [17:54:59] Test SparseIntVect ------------------------------------ +8: [17:54:59] Test SparseIntVect Serialization -------------------------- +8: [17:54:59] Test BitVect Serialization ------------------------------- +8: [17:54:59] Test BitVect to FPS ------------------------------- +8: [17:54:59] Test BitVect to binary string ------------------------------- +8: [17:54:59] Test Similarity Measures BitVect ------------------------------- +8: [17:54:59] Test Similarity Measures SparseBitVect ------------------------------- +8: [17:54:59] Test BitVect with all ones ------------------------------- +8: [17:54:59] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [17:54:59] Test bitmap operations ------------------------------- +8: [17:54:59] Test bitmaps as properties ------------------------------- +8: [17:54:59] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +11: Randomness seeded to: 3777263678 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -16479,8 +16647,8 @@ 16: testPointOps2D 16: **************************************** 16: test12D -16: ref1: 1.0719 4.54672 ref2: 4.83545 4.43335 -16: pt1: 2.16668 1.2005 pt2: 4.03205 3.84592 +16: ref1: 3.12055 3.47906 ref2: 0.310595 4.63828 +16: pt1: 1.85458 3.61071 pt2: 1.23918 3.56362 16: **************************************** 16: test23D 16: **************************************** @@ -16495,77 +16663,6 @@ 16: **************************************** 16: testFromQuaternion 16: **************************************** -20: [09:08:12] ----------------------------------------- -20: [09:08:12] Testing RDNumerics: vectors and matrices Code -20: [09:08:12] --------------------------------------- -20: [09:08:12] test1Vector -20: [09:08:12] --------------------------------------- -20: [09:08:12] test2Matrix -20: [09:08:12] --------------------------------------- -20: [09:08:12] test3SquareMatrix -20: [09:08:12] --------------------------------------- -20: [09:08:12] test4SymmMatrix - 1/230 Test #4: testRDValue ............................ Passed 0.05 sec - 2/230 Test #6: dictTestsCatch ......................... Passed 0.05 sec - 3/230 Test #7: logTestsCatch .......................... Passed 0.05 sec - 4/230 Test #8: testDataStructs ........................ Passed 0.04 sec - 5/230 Test #9: testFPB ................................ Passed 0.04 sec - 6/230 Test #10: testMultiFPB ........................... Passed 0.04 sec - 7/230 Test #11: catchDataStructs ....................... Passed 0.04 sec - 8/230 Test #16: testTransforms ......................... Passed 0.02 sec -test 21 - Start 21: testConrec - -21: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/testConrec -21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment -22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Numerics/Alignment -22: Test timeout computed to be: 1500 -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-x86_64-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-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch -25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField -26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/ForceField/Wrap -28: Test timeout computed to be: 1500 -18: Randomness seeded to: 4075087753 -18: =============================================================================== -18: All tests passed (50 assertions in 5 test cases) -18: - 9/230 Test #18: geometryTestsCatch ..................... Passed 0.07 sec 17: *********************************************************** 17: Testing Grid 17: --------------------------------- @@ -16583,6 +16680,24 @@ 17: --------------------------------- 17: testUniformGridIndexing 17: +18: Randomness seeded to: 2990185254 +18: =============================================================================== +18: All tests passed (50 assertions in 5 test cases) +18: +20: [17:54:59] ----------------------------------------- +20: [17:54:59] Testing RDNumerics: vectors and matrices Code +20: [17:54:59] --------------------------------------- +20: [17:54:59] test1Vector +20: [17:54:59] --------------------------------------- +20: [17:54:59] test2Matrix +20: [17:54:59] --------------------------------------- +20: [17:54:59] test3SquareMatrix +20: [17:54:59] --------------------------------------- +20: [17:54:59] test4SymmMatrix +21: Randomness seeded to: 341685163 +21: =============================================================================== +21: All tests passed (76 assertions in 3 test cases) +21: 22: ----------------------------------------- 22: Testing Alignment Code 22: --------------------------------------- @@ -16600,6 +16715,10 @@ 24: ------------------------------------- 24: Testing BFGS optimization. 24: done +25: Randomness seeded to: 1651129778 +25: =============================================================================== +25: All tests passed (20 assertions in 2 test cases) +25: 26: ------------------------------------- 26: Unit tests for force field basics. 26: done @@ -16648,49 +16767,6 @@ 26: Unit tests for all UFF constraint terms. 27: ------------------------------------- 27: Official MMFF validation suite. - 10/230 Test #17: testGrid ............................... Passed 0.07 sec - 11/230 Test #20: testMatrices ........................... Passed 0.06 sec - 12/230 Test #22: testAlignment .......................... Passed 0.05 sec - 13/230 Test #24: testOptimizer .......................... Passed 0.04 sec -test 29 - Start 29: testDistGeom - -29: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom -29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest -32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -test 33 - Start 33: graphmolqueryTest - -33: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -33: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -25: Randomness seeded to: 2277183330 -25: =============================================================================== -25: All tests passed (20 assertions in 2 test cases) -25: -3: static boost any:0.115242 s -21: Randomness seeded to: 3525788632 -21: =============================================================================== -21: All tests passed (76 assertions in 3 test cases) -21: 29: *********************************************************** 29: test1 29: *********************************************************** @@ -16702,31 +16778,6 @@ 29: 1 1 1 0 29: *********************************************************** 29: - 14/230 Test #21: testConrec ............................. Passed 0.12 sec - 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.10 sec - 16/230 Test #29: testDistGeom ........................... Passed 0.07 sec -test 34 - Start 34: graphmolMolOpsTest - -34: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -test 35 - Start 35: graphmoltestChirality - -35: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality -35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -test 36 - Start 36: graphmoltestPickler - -36: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler -36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -32: -32: -32: -32: COPY 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: @@ -16745,7 +16796,7 @@ 31: 4 5->6 order: 3 31: 5 6->7 order: 1 31: 6 7->8 order: 2 -31: [09:08:12] +31: [17:54:59] 31: 31: **** 31: Pre-condition Violation @@ -16757,15 +16808,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x00005631E6C5602C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776D902C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776D3041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:12] +31: [17:54:59] 31: 31: **** 31: Pre-condition Violation @@ -16777,15 +16828,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x00005631E6C442F8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776C72F8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776D3041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:12] +31: [17:54:59] 31: 31: **** 31: Pre-condition Violation @@ -16797,15 +16848,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x00005631E6C444DE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776C74DE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776D3041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:12] +31: [17:54:59] 31: 31: **** 31: Pre-condition Violation @@ -16817,15 +16868,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x00005631E6C4451B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776C751B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776D3041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:12] +31: [17:54:59] 31: 31: **** 31: Pre-condition Violation @@ -16837,17 +16888,17 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x00005631E6C4464E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C50041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776C764E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776D3041 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 7# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:12] Explicit valence for atom # 0 B, 4, is greater than permitted -31: [09:08:12] Explicit valence for atom # 0 B, 4, is greater than permitted -31: [09:08:13] +31: [17:54:59] Explicit valence for atom # 0 B, 4, is greater than permitted +31: [17:54:59] Explicit valence for atom # 0 B, 4, is greater than permitted +31: [17:54:59] 31: 31: **** 31: Post-condition Violation @@ -16859,73 +16910,1080 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x00005631E6C78917 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00005631E6C614DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x00005631E6C50050 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 6# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 3# 0x0000557E776FB917 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000557E776E44DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000557E776D3050 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 31: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 8# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 8# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test github381: thread-safe initialization of the periodic table -33: [09:08:13] ---------------------- Test1 -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test2 -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test3 -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test4 -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test5 -33: [09:08:13] Done! -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test issue 2892580 -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test github issue 53: query molecules not matching [R] -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test queries using qualifiers instead of == -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test extra atom queries -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test extra bond queries -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test num heteroatom neighbor queries -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test atom type queries -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -33: [09:08:13] Done! -33: [09:08:13] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -33: [09:08:13] Done! +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test github381: thread-safe initialization of the periodic table +32: +32: +32: +32: COPY +33: [17:54:59] ---------------------- Test1 +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test2 +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test3 +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test4 +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test5 +33: [17:54:59] Done! +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test issue 2892580 +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test github issue 53: query molecules not matching [R] +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test queries using qualifiers instead of == +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test extra atom queries +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test extra bond queries +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test num heteroatom neighbor queries +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test atom type queries +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +33: [17:54:59] Done! +33: [17:54:59] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +33: [17:54:59] Done! +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing String Pickle Roundtrips. + 1/230 Test #4: testRDValue ............................ Passed 0.07 sec + 2/230 Test #6: dictTestsCatch ......................... Passed 0.07 sec + 3/230 Test #7: logTestsCatch .......................... Passed 0.07 sec + 4/230 Test #8: testDataStructs ........................ Passed 0.06 sec + 5/230 Test #9: testFPB ................................ Passed 0.06 sec + 6/230 Test #10: testMultiFPB ........................... Passed 0.06 sec + 7/230 Test #11: catchDataStructs ....................... Passed 0.06 sec + 8/230 Test #16: testTransforms ......................... Passed 0.05 sec + 9/230 Test #17: testGrid ............................... Passed 0.05 sec + 10/230 Test #18: geometryTestsCatch ..................... Passed 0.05 sec + 11/230 Test #20: testMatrices ........................... Passed 0.05 sec + 12/230 Test #21: testConrec ............................. Passed 0.05 sec + 13/230 Test #22: testAlignment .......................... Passed 0.04 sec + 14/230 Test #24: testOptimizer .......................... Passed 0.04 sec + 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.04 sec + 16/230 Test #29: testDistGeom ........................... Passed 0.03 sec + 17/230 Test #32: graphmolcpTest ......................... Passed 0.03 sec + 18/230 Test #33: graphmolqueryTest ...................... Passed 0.03 sec +test 43 + Start 43: testSGroup + +43: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup +43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +test 44 + Start 44: test-valgrind + +44: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind +44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +test 45 + Start 45: graphmolTestsCatch + +45: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +test 46 + Start 46: graphmolOrganometallicsCatch + +46: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +test 47 + Start 47: graphmolSGroupCatch + +47: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +test 48 + Start 48: graphmolAdjustQueryCatch + +48: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +test 49 + Start 49: chiralityTestsCatch + +49: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch +49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +test 50 + Start 50: canonTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 +test 51 + Start 51: moliteratorTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +test 52 + Start 52: queryTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +test 53 + Start 53: molbundleTestsCatch + +53: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 +test 54 + Start 54: pickleTestsCatch + +54: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch +54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol +54: Test timeout computed to be: 1500 +test 55 + Start 55: tableTestsCatch + +55: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch +55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch +56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +57: Test timeout computed to be: 1500 +test 58 + Start 58: smiTest2 + +58: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +58: Test timeout computed to be: 1500 +test 59 + Start 59: cxsmilesTest + +59: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +59: Test timeout computed to be: 1500 +test 60 + Start 60: smaTest1 + +60: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +60: Test timeout computed to be: 1500 +3: static boost any:0.063005 s 26: done 26: ------------------------------------- 26: Unit tests for copying UFF ForceFields. - 17/230 Test #32: graphmolcpTest ......................... Passed 0.08 sec -test 37 - Start 37: graphmoltestPicklerGlobalSetting - -37: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 26: done 26: ------------------------------------- 26: Unit test for UFF butane scan. - 18/230 Test #33: graphmolqueryTest ...................... Passed 0.07 sec -test 38 - Start 38: graphmolIterTest - -38: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest -38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 +31: [17:54:59] done +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [17:54:59] +31: +31: **** +31: Pre-condition Violation +31: no owner +31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +31: Failed Expression: dp_mol +31: ---------- +31: Stacktrace: +31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 2# 0x0000557E776F1B9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000557E776D307D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +31: 6# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: ---------- +31: **** +31: +31: [17:54:59] +31: +31: **** +31: Pre-condition Violation +31: no owner +31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +31: Failed Expression: dp_mol +31: ---------- +31: Stacktrace: +31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 2# 0x0000557E776D2979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000557E776D307D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +31: 6# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: ---------- +31: **** +31: +31: [17:54:59] done +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [17:54:59] +31: +31: **** +31: Pre-condition Violation +31: no owner +31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +31: Failed Expression: dp_mol +31: ---------- +31: Stacktrace: +31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 2# 0x0000557E776F1B9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000557E776D3082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +31: 6# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: ---------- +31: **** +31: +31: [17:54:59] +31: +31: **** +31: Pre-condition Violation +31: no owner +31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +31: Failed Expression: dp_mol +31: ---------- +31: Stacktrace: +31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +31: 2# 0x0000557E776D2979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000557E776D3082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x00007F6278833D68 in /lib/x86_64-linux-gnu/libc.so.6 +31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +31: 6# 0x0000557E776D30E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +31: ---------- +31: **** +31: +31: [17:54:59] done +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test github1453: RWMol.clear() should reset the numBonds count. +31: [17:54:59] done +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test range-based for loops. +31: [17:54:59] done +31: [17:54:59] ------------------------------------- +31: [17:54:59] Test github1642: Atom index type is too low for big molecules. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing reading existing pickle file (v2). +34: 1 1 2 +34: 1 1 1 +34: 2 1 0.75 +34: path: 2 +34: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +34: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +34: [17:54:59] Explicit valence for atom # 0 B, 5, is greater than permitted +34: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [17:54:59] Explicit valence for atom # 1 Si, 7, is greater than permitted 35: -------------------------- 35: -------------------------- 35: C/C=C/C(C)Cl -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing String Pickle Roundtrips. +35: [17:54:59] Conflicting single bond directions around double bond at index 2. +35: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [17:54:59] Conflicting single bond directions around double bond at index 4. +35: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [17:54:59] Conflicting single bond directions around double bond at index 15. +35: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [17:54:59] Conflicting single bond directions around double bond at index 2. +35: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [17:54:59] Conflicting single bond directions around double bond at index 1. +35: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +35: -------------------------------------------------- + 19/230 Test #40: graphmolMemTest1 ....................... Passed 0.08 sec +37: [17:54:59] done + 20/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec + 21/230 Test #38: graphmolIterTest ....................... Passed 0.08 sec +39: [17:54:59] Testing the hanoi sort +39: [17:54:59] populating vectors +45: Randomness seeded to: 4203875090 +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 1 N, 6, is greater than permitted +45: [17:54:59] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [17:54:59] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [17:54:59] non-ring atom 2 marked aromatic +45: [17:54:59] non-ring atom 2 marked aromatic +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [17:54:59] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [17:54:59] Explicit valence for atom # 4 F, 2, is greater than permitted +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 +45: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [17:54:59] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [17:54:59] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [17:54:59] WARNING: not removing hydrogen atom with wedged bond +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] Unreasonable formal charge on atom # 0. +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156D7D8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156D862 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156D8F5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156D9E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156DA71 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156DB0D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156E429 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156DC78 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156DD12 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156E401 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156E028 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A156E3DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: not removing hydrogen atom without neighbors +45: [17:54:59] Explicit valence for atom # 1 F greater than permitted +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A1516E4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A1516EE0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A1516B70 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +45: 3# 0x00005647A1516C05 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x00005647A15BA938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x00005647A15BB458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x00005647A15BB8D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x00005647A158D0C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x00005647A158D42C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x00005647A150945E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x00007EFFDDC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +45: 12# 0x00005647A15094A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: ---------- +45: **** +45: +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: Randomness seeded to: 3264719862 +47: =============================================================================== +47: All tests passed (136 assertions in 8 test cases) +47: +51: Randomness seeded to: 465102477 +51: =============================================================================== +51: All tests passed (14 assertions in 4 test cases) +51: +52: Randomness seeded to: 1321133309 +52: =============================================================================== +52: All tests passed (10 assertions in 1 test case) +52: + 22/230 Test #35: graphmoltestChirality .................. Passed 0.09 sec + 23/230 Test #42: molBundleTest .......................... Passed 0.08 sec + 24/230 Test #43: testSGroup ............................. Passed 0.07 sec + 25/230 Test #44: test-valgrind .......................... Passed 0.07 sec + 26/230 Test #47: graphmolSGroupCatch .................... Passed 0.06 sec + 27/230 Test #51: moliteratorTestsCatch .................. Passed 0.05 sec + 28/230 Test #52: queryTestsCatch ........................ Passed 0.05 sec +test 61 + Start 61: smiTestCatch + +61: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +62: Test timeout computed to be: 1500 +test 63 + Start 63: v2smiTestCatch + +63: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +test 64 + Start 64: testDepictor + +64: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +64: Test timeout computed to be: 1500 +test 65 + Start 65: depictorCatch + +65: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +test 66 + Start 66: pyDepictor + +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-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +66: Test timeout computed to be: 1500 +test 67 + Start 67: testMrvToMol + +67: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse +67: Test timeout computed to be: 1500 +test 68 + Start 68: fileParsersTest1 + +68: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +test 69 + Start 69: testAtropisomers + +69: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +test 70 + Start 70: testSquiggleDoubleBonds + +70: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] 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 +36: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +36: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +36: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +36: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 +36: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +36: Bonds: +36: 0 0->1 order: 1 +36: 1 1->2 order: 1 +36: 2 2->0 order: 1 +36: 3 3->4 order: 1 +36: 4 4->5 order: 1 +36: 5 5->6 order: 1 +36: 6 6->3 order: 1 +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Issue164: Roundtrip Pickle Failure. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Issue219: Pickle Failure with Conformations. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Issue220: Pickle problems with bond stereochemistry. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing query serialization. +36: [17:54:59] C=[$(C=O)] +36: [17:54:59] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing radical handling in pickles. +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 2788233. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 3202580. +36: mass! 13.0034 +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 3316407. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 3496759. +36: smi match: *C *C +36: smi match: **=* **=* +36: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O +36: smi match: *OS(=O)OC *OS(=O)OC +36: smi match: *S(=O)(=O)OC *S(=O)(=O)OC +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 +36: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 +36: smi match: nnnOC=O nnnOC=O +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 +36: smi match: NP(N)(N)=O NP(N)(N)=O +36: smi match: cN=[N+]=[N-] cN=[N+]=[N-] +36: smi match: *CC=O *CC=O +36: smi match: NNC=O NNC=O +36: smi match: * * +36: smi match: C=P C=P +36: smi match: CC(=N)Cl CC(=N)Cl +36: smi match: N=O N=O +36: smi match: ** ** +36: smi match: N=C=N N=C=N +36: smi match: [C-]#[NH+] [C-]#[NH+] +36: smi match: O=CON(C=O)C=O O=CON(C=O)C=O +36: smi match: N#CC[OH] N#CC[OH] +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 +36: smi match: OCCOCCO OCCOCCO +36: smi match: SS SS +36: smi match: [SH] [SH] +36: smi match: *1CC1 *1CC1 +36: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] +36: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] +36: smi match: NC(=S)N=N NC(=S)N=N +36: smi match: N#CS N#CS +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 +36: smi match: O=C1CCO1 O=C1CCO1 +36: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] +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 +36: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 +36: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 +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 +36: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 +36: smi match: cN(=O)~O cN(=O)~O +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 +36: smi match: CO*(=O)=O CO*(=O)=O +36: smi match: * * +36: smi match: * * +36: smi match: *C=C *C=C +36: smi match: N#CS N#CS +36: smi match: *C=S *C=S +36: smi match: *N *N +36: smi match: *C(=C)C=O *C(=C)C=O +36: smi match: *C#C *C#C +36: smi match: N#CCO N#CCO +36: smi match: O=N(=O)CCO O=N(=O)CCO +36: smi match: N=CS N=CS +36: smi match: O=CNC(O)C=O O=CNC(O)C=O +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 +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 +36: smi match: O=CN(S)C=O O=CN(S)C=O +36: smi match: O=CNC=O O=CNC=O +36: smi match: O=CNN=O O=CNN=O +36: smi match: O=CNNC=O O=CNNC=O +36: smi match: O=CNOC=O O=CNOC=O +36: smi match: O=CS O=CS +36: smi match: O=CSC=S O=CSC=S +36: smi match: S=CS S=CS +36: smi match: C=O C=O +36: smi match: *C=N *C=N +36: smi match: CCCCCCC CCCCCCC +36: smi match: CN=O CN=O +36: smi match: CS(=O)(=O)O CS(=O)(=O)O +36: smi match: O=C1CCO1 O=C1CCO1 +36: smi match: C=C(S)[SH]=O C=C(S)[SH]=O +36: smi match: C=CCO C=CCO +36: smi match: C=CC=N C=CC=N +36: smi match: C=CC=O C=CC=O +36: smi match: C=CC(=O)C=C C=CC(=O)C=C +36: smi match: C=CC=S C=CC=S +36: smi match: C=CC(=S)S C=CC(=S)S +36: smi match: *C=C(*)C=C *C=C(*)C=C +36: smi match: C=CC=N C=CC=N +36: smi match: *N(*)C=C *N(*)C=C +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: C=CO C=CO +36: smi match: C=COC=O C=COC=O +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 +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 +36: smi match: C=NO C=NO +36: smi match: C=NOC=O C=NOC=O +36: smi match: C=N=O C=N=O +36: smi match: N#CS N#CS +36: smi match: *CN=O *CN=O +36: smi match: NCN NCN +36: smi match: ON=CCN=O ON=CCN=O +36: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O +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 +36: smi match: NC(N)=S NC(N)=S +36: smi match: C=CN C=CN +36: smi match: NOC=O NOC=O +36: smi match: C1CN1 C1CN1 +36: smi match: O=C1NNNN1 O=C1NNNN1 +36: smi match: N=C(N)C(=N)N N=C(N)C(=N)N +36: smi match: N=C(N)O N=C(N)O +36: smi match: N=C(N)C(=N)S N=C(N)C(=N)S +36: smi match: *C=N *C=N +36: smi match: N=CC=O N=CC=O +36: smi match: N=CS N=CS +34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +34: [17:54:59] non-ring atom 0 marked aromatic +34: [17:54:59] non-ring atom 0 marked aromatic +45: [17:54:59] Unusual charge on atom 0 number of radical electrons set to zero +45: [17:54:59] Unusual charge on atom 0 number of radical electrons set to zero +45: [17:54:59] Unusual charge on atom 0 number of radical electrons set to zero +45: [17:54:59] non-ring atom 0 marked aromatic +45: [17:54:59] non-ring atom 0 marked aromatic +45: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 3 N, 4, is greater than permitted +45: [17:54:59] Explicit valence for atom # 15 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 11 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [17:54:59] Explicit valence for atom # 9 C, 6, is greater than permitted +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 7 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 3 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 3 7 +45: [17:54:59] Can't kekulize mol. Unkekulized atoms: 3 7 +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [17:54:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [17:54:59] SMILES Parse Error: syntax error while parsing: - +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [17:54:59] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +58: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 29/230 Test #58: smiTest2 ............................... Passed 0.06 sec +53: Randomness seeded to: 1196409847 +53: =============================================================================== +53: All tests passed (6 assertions in 1 test case) +53: + 30/230 Test #53: molbundleTestsCatch .................... Passed 0.08 sec +55: Randomness seeded to: 1287206796 +55: =============================================================================== +55: All tests passed (7 assertions in 2 test cases) +55: + 31/230 Test #55: tableTestsCatch ........................ Passed 0.07 sec +56: Randomness seeded to: 1094562460 +56: =============================================================================== +56: All tests passed (72 assertions in 4 test cases) +56: + 32/230 Test #56: molopsTestsCatch ....................... Passed 0.07 sec +49: Randomness seeded to: 2057117896 +49: [17:54:59] unable to set wavy bonds for double bonds: 3 +49: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: [17:54:59] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: [17:54:59] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: [17:54:59] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +49: =============================================================================== +49: All tests passed (2267 assertions in 79 test cases) +49: 1: cyclosporine a 1: RDKit 2D 1: @@ -17141,7 +18199,6 @@ 1: 16 17 1 0 1: M END 1: -37: [09:08:13] done 1: cis-trans 1: RDKit 2D 1: @@ -17195,27 +18252,6 @@ 1: 10 2 1 0 1: M END 1: -35: [09:08:13] Conflicting single bond directions around double bond at index 2. -35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [09:08:13] Conflicting single bond directions around double bond at index 4. -35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [09:08:13] Conflicting single bond directions around double bond at index 15. -35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [09:08:13] Conflicting single bond directions around double bond at index 2. -35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [09:08:13] Conflicting single bond directions around double bond at index 1. -35: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -34: 1 1 2 -34: 1 1 1 -34: 2 1 0.75 -34: path: 2 - 19/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec -test 39 - Start 39: hanoiTest - -39: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest -39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -17308,708 +18344,113 @@ 1: 30 11 1 0 1: M END 1: -34: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -34: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: -------------------------------------------------- 27: 27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... - 20/230 Test #35: graphmoltestChirality .................. Passed 0.09 sec -test 40 - Start 40: graphmolMemTest1 - -40: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -31: [09:08:13] done -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [09:08:13] -31: -31: **** -31: Pre-condition Violation -31: no owner -31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -31: Failed Expression: dp_mol -31: ---------- -31: Stacktrace: -31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x00005631E6C6EB9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x00005631E6C5007D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 -31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: ---------- -31: **** -31: -31: [09:08:13] -31: -31: **** -31: Pre-condition Violation -31: no owner -31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -31: Failed Expression: dp_mol -31: ---------- -31: Stacktrace: -31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x00005631E6C4F979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x00005631E6C5007D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 -31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: ---------- -31: **** -31: -31: [09:08:13] done -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [09:08:13] -31: -31: **** -31: Pre-condition Violation -31: no owner -31: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -31: Failed Expression: dp_mol -31: ---------- -31: Stacktrace: -31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x00005631E6C6EB9B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x00005631E6C50082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 -31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: ---------- -31: **** -31: -31: [09:08:13] -31: -31: **** -31: Pre-condition Violation -31: no owner -31: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -31: Failed Expression: dp_mol -31: ---------- -31: Stacktrace: -31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x00005631E6C4F979 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x00005631E6C50082 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x00007FA3F0031D68 in /lib/x86_64-linux-gnu/libc.so.6 -31: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -31: 6# 0x00005631E6C500E1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -31: ---------- -31: **** -31: -31: [09:08:13] done -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test github1453: RWMol.clear() should reset the numBonds count. -31: [09:08:13] done -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test range-based for loops. -31: [09:08:13] done -31: [09:08:13] ------------------------------------- -31: [09:08:13] Test github1642: Atom index type is too low for big molecules. -34: [09:08:13] Explicit valence for atom # 0 B, 5, is greater than permitted - 21/230 Test #38: graphmolIterTest ....................... Passed 0.06 sec -test 41 - Start 41: resMolSupplierTest +54: Randomness seeded to: 2353224311 +54: =============================================================================== +54: All tests passed (45 assertions in 4 test cases) +54: + 33/230 Test #54: pickleTestsCatch ....................... Passed 0.08 sec +46: Randomness seeded to: 857366878 +46: =============================================================================== +46: All tests passed (62 assertions in 6 test cases) +46: + 34/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.10 sec +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] WARNING: not removing hydrogen atom without neighbors +57: [17:54:59] Invalid chiral specification on atom 0 +57: [17:54:59] Invalid chiral specification on atom 0 +57: [17:54:59] Invalid chiral specification on atom 0 +57: [17:54:59] Invalid chiral specification on atom 0 +57: [17:54:59] Invalid chiral specification on atom 0 +57: [17:54:59] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +57: [17:54:59] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +48: Randomness seeded to: 1411981210 +48: =============================================================================== +48: All tests passed (281 assertions in 10 test cases) +48: + 35/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.09 sec +61: Randomness seeded to: 2041243068 +61: [17:54:59] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +61: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [17:54:59] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +61: [17:54:59] SMARTS Parse Error: unclosed ring for input: 'C1C' +61: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [17:54:59] SMARTS Parse Error: syntax error while parsing: C)foo +61: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +61: [17:54:59] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +61: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: Randomness seeded to: 3969273457 +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [17:54:59] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: Randomness seeded to: 3476841781 +63: =============================================================================== +63: All tests passed (14 assertions in 2 test cases) +63: + 36/230 Test #1: testCoordGen ........................... Passed 0.18 sec +test 71 + Start 71: testMolSupplier -41: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [09:08:13] Explicit valence for atom # 1 Si, 7, is greater than permitted -39: [09:08:13] Testing the hanoi sort -39: [09:08:13] populating vectors - 22/230 Test #1: testCoordGen ........................... Passed 0.33 sec - 23/230 Test #40: graphmolMemTest1 ....................... Passed 0.03 sec -test 42 - Start 42: molBundleTest +71: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +test 72 + Start 72: testGeneralFileReader -42: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest -42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -test 43 - Start 43: testSGroup +72: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +test 73 + Start 73: testMultithreadedMolSupplier -43: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup -43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing reading existing pickle file (v2). -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.011s -14: -14: OK -23: ..... -23: ---------------------------------------------------------------------- -23: Ran 5 tests in 0.002s -23: -23: OK -23: Testing Alignment Wrapper code: - 24/230 Test #42: molBundleTest .......................... Passed 0.07 sec -test 44 - Start 44: test-valgrind +73: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +test 74 + Start 74: testMolWriter -44: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind -44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.052s -15: -15: OK -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] 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 -36: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -36: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -36: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -36: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 -36: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -36: Bonds: -36: 0 0->1 order: 1 -36: 1 1->2 order: 1 -36: 2 2->0 order: 1 -36: 3 3->4 order: 1 -36: 4 4->5 order: 1 -36: 5 5->6 order: 1 -36: 6 6->3 order: 1 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Issue164: Roundtrip Pickle Failure. -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.041s -2: -2: OK -19: ........... -19: ---------------------------------------------------------------------- -19: Ran 11 tests in 0.056s -19: -19: OK -19: Testing Geometry wrapper -30: ...... -30: ---------------------------------------------------------------------- -30: Ran 6 tests in 0.001s -30: -30: OK - 25/230 Test #43: testSGroup ............................. Passed 0.11 sec -test 45 - Start 45: graphmolTestsCatch +74: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +test 75 + Start 75: testTplParser -45: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Issue219: Pickle Failure with Conformations. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Issue220: Pickle problems with bond stereochemistry. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing query serialization. -36: [09:08:13] C=[$(C=O)] -36: [09:08:13] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing radical handling in pickles. -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 2788233. - 26/230 Test #14: pySparseIntVect ........................ Passed 0.44 sec - 27/230 Test #23: pyAlignment ............................ Passed 0.40 sec -test 46 - Start 46: graphmolOrganometallicsCatch +75: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +test 76 + Start 76: testMol2ToMol -46: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -test 47 - Start 47: graphmolSGroupCatch +76: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +test 77 + Start 77: testSequence -47: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 3202580. -36: mass! 13.0034 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 3316407. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 3496759. -36: smi match: *C *C -36: smi match: **=* **=* -36: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O -36: smi match: *OS(=O)OC *OS(=O)OC -36: smi match: *S(=O)(=O)OC *S(=O)(=O)OC -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 -36: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 -36: smi match: nnnOC=O nnnOC=O -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 -36: smi match: NP(N)(N)=O NP(N)(N)=O -36: smi match: cN=[N+]=[N-] cN=[N+]=[N-] -36: smi match: *CC=O *CC=O -36: smi match: NNC=O NNC=O -36: smi match: * * -36: smi match: C=P C=P -36: smi match: CC(=N)Cl CC(=N)Cl -36: smi match: N=O N=O -36: smi match: ** ** -36: smi match: N=C=N N=C=N -36: smi match: [C-]#[NH+] [C-]#[NH+] -36: smi match: O=CON(C=O)C=O O=CON(C=O)C=O -36: smi match: N#CC[OH] N#CC[OH] -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 -36: smi match: OCCOCCO OCCOCCO -36: smi match: SS SS -36: smi match: [SH] [SH] -36: smi match: *1CC1 *1CC1 -36: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] -36: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] -36: smi match: NC(=S)N=N NC(=S)N=N -36: smi match: N#CS N#CS -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 -36: smi match: O=C1CCO1 O=C1CCO1 -36: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] -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 -36: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 -36: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 -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 -36: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 -36: smi match: cN(=O)~O cN(=O)~O -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 -36: smi match: CO*(=O)=O CO*(=O)=O -36: smi match: * * -36: smi match: * * -36: smi match: *C=C *C=C -36: smi match: N#CS N#CS -36: smi match: *C=S *C=S -36: smi match: *N *N -45: Randomness seeded to: 3206593127 -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 N, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [09:08:13] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [09:08:13] non-ring atom 2 marked aromatic -45: [09:08:13] non-ring atom 2 marked aromatic -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [09:08:13] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [09:08:13] Explicit valence for atom # 4 F, 2, is greater than permitted -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 - 28/230 Test #44: test-valgrind .......................... Passed 0.10 sec -test 48 - Start 48: graphmolAdjustQueryCatch +77: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +test 78 + Start 78: testExtendedStereoParsing -48: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -36: smi match: *C(=C)C=O *C(=C)C=O -36: smi match: *C#C *C#C -36: smi match: N#CCO N#CCO -36: smi match: O=N(=O)CCO O=N(=O)CCO -36: smi match: N=CS N=CS -36: smi match: O=CNC(O)C=O O=CNC(O)C=O -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 -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 -36: smi match: O=CN(S)C=O O=CN(S)C=O -36: smi match: O=CNC=O O=CNC=O -36: smi match: O=CNN=O O=CNN=O -36: smi match: O=CNNC=O O=CNNC=O -36: smi match: O=CNOC=O O=CNOC=O -36: smi match: O=CS O=CS -36: smi match: O=CSC=S O=CSC=S -36: smi match: S=CS S=CS -36: smi match: C=O C=O -36: smi match: *C=N *C=N -36: smi match: CCCCCCC CCCCCCC -36: smi match: CN=O CN=O -36: smi match: CS(=O)(=O)O CS(=O)(=O)O -36: smi match: O=C1CCO1 O=C1CCO1 -36: smi match: C=C(S)[SH]=O C=C(S)[SH]=O -36: smi match: C=CCO C=CCO -36: smi match: C=CC=N C=CC=N -36: smi match: C=CC=O C=CC=O -36: smi match: C=CC(=O)C=C C=CC(=O)C=C -36: smi match: C=CC=S C=CC=S -36: smi match: C=CC(=S)S C=CC(=S)S -45: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted -45: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [09:08:13] WARNING: not removing hydrogen atom with wedged bond -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] Unreasonable formal charge on atom # 0. -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x00005652782927D8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278292862 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x00005652782928F5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x00005652782929E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278292A71 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278292B0D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278293429 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278292C78 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278292D12 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278293401 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000565278293028 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -34: [09:08:13] non-ring atom 0 marked aromatic -34: [09:08:13] non-ring atom 0 marked aromatic -34: [09:08:13] Conflicting single bond directions around double bond at index 17. -34: [09:08:13] BondStereo set to STEREONONE and single bond directions set to NONE. -34: starting ring finding -34: done -34: starting ring finding -34: done -34: starting ring finding -36: smi match: *C=C(*)C=C *C=C(*)C=C -36: smi match: C=CC=N C=CC=N -36: smi match: *N(*)C=C *N(*)C=C -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: C=CO C=CO -36: smi match: C=COC=O C=COC=O -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 -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 -36: smi match: C=NO C=NO -36: smi match: C=NOC=O C=NOC=O -36: smi match: C=N=O C=N=O -36: smi match: N#CS N#CS -36: smi match: *CN=O *CN=O -36: smi match: NCN NCN -36: smi match: ON=CCN=O ON=CCN=O -36: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O -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 -36: smi match: NC(N)=S NC(N)=S -36: smi match: C=CN C=CN -36: smi match: NOC=O NOC=O -36: smi match: C1CN1 C1CN1 -36: smi match: O=C1NNNN1 O=C1NNNN1 -36: smi match: N=C(N)C(=N)N N=C(N)C(=N)N -36: smi match: N=C(N)O N=C(N)O -36: smi match: N=C(N)C(=N)S N=C(N)C(=N)S -36: smi match: *C=N *C=N -36: smi match: N=CC=O N=CC=O -36: smi match: N=CS N=CS +78: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 36: smi match: N=C=N N=C=N 36: smi match: N=C=O N=C=O 36: smi match: N=C=S N=C=S @@ -18051,167 +18492,6 @@ 36: smi match: N#CS N#CS 36: smi match: C=NO C=NO 36: smi match: C=N[SH]=N C=N[SH]=N -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x00005652782933DD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: not removing hydrogen atom without neighbors -45: [09:08:13] Explicit valence for atom # 1 F greater than permitted -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x000056527823BE4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x000056527823BEE0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x000056527823BB70 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x000056527823BC05 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x00005652782DF938 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x00005652782E0458 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x00005652782E08D0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x00005652782B20C3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x00005652782B242C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x000056527822E45E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x00007F414D831D68 in /lib/x86_64-linux-gnu/libc.so.6 -45: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -45: 12# 0x000056527822E4A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: ---------- -45: **** -45: -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero -45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero -45: [09:08:13] Unusual charge on atom 0 number of radical electrons set to zero -45: [09:08:13] non-ring atom 0 marked aromatic -45: [09:08:13] non-ring atom 0 marked aromatic -45: [09:08:13] Explicit valence for atom # 1 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 3 N, 4, is greater than permitted -45: [09:08:13] Explicit valence for atom # 15 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 11 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [09:08:13] Explicit valence for atom # 9 C, 6, is greater than permitted -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 7 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 7 -45: [09:08:13] Can't kekulize mol. Unkekulized atoms: 3 7 -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [09:08:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 29/230 Test #30: pyDistGeom ............................. Passed 0.45 sec -test 49 - Start 49: chiralityTestsCatch - -49: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch -49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 36: smi match: O=C(S)S O=C(S)S 36: smi match: N=C(S)S N=C(S)S 36: smi match: N=C(=N)S N=C(=N)S @@ -18261,35 +18541,6 @@ 36: smi match: OOO OOO 36: smi match: OO OO 36: smi match: O~Cl(~O)~O O~Cl(~O)~O -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 - 30/230 Test #19: testPyGeometry ......................... Passed 0.54 sec -3: dynamic boost any:0.387596 s - 31/230 Test #15: pyFPB .................................. Passed 0.55 sec - 32/230 Test #2: pyCoordGen ............................. Passed 0.59 sec -47: Randomness seeded to: 1111466049 -47: =============================================================================== -47: All tests passed (136 assertions in 8 test cases) -47: -test 50 - Start 50: canonTestsCatch - -50: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -test 51 - Start 51: moliteratorTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -test 52 - Start 52: queryTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 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 @@ -18328,32 +18579,6 @@ 36: smi match: *C(*)C=O *C(*)C=O 36: smi match: *CC=O *CC=O 36: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -34: done -34: starting sanitization -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 -46: Randomness seeded to: 2855683568 -46: =============================================================================== -46: All tests passed (62 assertions in 6 test cases) -46: - 33/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.13 sec - 34/230 Test #47: graphmolSGroupCatch .................... Passed 0.12 sec -test 53 - Start 53: molbundleTestsCatch - -53: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch -53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -53: Test timeout computed to be: 1500 -test 54 - Start 54: pickleTestsCatch - -54: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch -54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol -54: Test timeout computed to be: 1500 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 @@ -18361,6 +18586,93 @@ 36: smi match: *1CC1 *1CC1 36: smi match: O=COC=O O=COC=O 36: smi match: N=C=O N=C=O +34: [17:54:59] Conflicting single bond directions around double bond at index 17. +34: [17:54:59] BondStereo set to STEREONONE and single bond directions set to NONE. +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 +34: done +34: starting sanitization + 37/230 Test #49: chiralityTestsCatch .................... Passed 0.12 sec +61: [17:54:59] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +62: [17:54:59] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +62: =============================================================================== +62: All tests passed (308 assertions in 9 test cases) +62: + 38/230 Test #63: v2smiTestCatch ......................... Passed 0.06 sec +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.005s +14: +14: OK +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.002s +13: +13: OK +69: [17:54:59] ---- Running with POSIX locale ----- +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.004s +15: +15: OK +23: ..... +23: ---------------------------------------------------------------------- +23: Ran 5 tests in 0.001s +23: +23: OK +23: Testing Alignment Wrapper code: +70: Randomness seeded to: 1473404382 +70: =============================================================================== +70: All tests passed (15 assertions in 3 test cases) +70: +68: *************************************** +68: *************************************** +68: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [17:54:59] +71: ----------------------------------------- +72: [17:54:59] +72: ----------------------------------------- +72: [17:54:59] Finished: testDetermineFormat() +72: [17:54:59] ----------------------------------------- +72: +72: [17:54:59] +72: ----------------------------------------- + 39/230 Test #62: nontetrahedralCatch .................... Passed 0.06 sec + 40/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.04 sec +test 79 + Start 79: fileParsersCatchTest + +79: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 +test 80 + Start 80: testPropertyLists + +80: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 +test 81 + Start 81: XYZFileParserCatchTest + +81: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +test 82 + Start 82: cdxmlParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 36: smi match: N=C=S N=C=S 36: smi match: O~O O~O 36: smi match: N~[SiH4] N~[SiH4] @@ -18405,6 +18717,41 @@ 36: smi match: *N=C(*)* *N=C(*)* 36: smi match: *C(*)(*)C=O *C(*)(*)C=O 36: smi match: CSC=O CSC=O +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 +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [17:54:59] bond with order 0 found on line 7. This is not part of the MDL specification. +73: [17:54:59] +73: ----------------------------------------- +45: [17:54:59] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [17:54:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [17:54:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:54:59] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +45: [17:54:59] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +45: [17:54:59] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +45: [17:54:59] non-ring atom 0 marked aromatic + 41/230 Test #13: pyDiscreteValueVect .................... Passed 0.20 sec + 42/230 Test #14: pySparseIntVect ........................ Passed 0.20 sec +test 83 + Start 83: molfileStereoCatchTest + +83: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +test 84 + Start 84: connectTheDotsTest + +84: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 36: smi match: * * 36: smi match: O=CCl O=CCl 36: smi match: *** *** @@ -18415,62 +18762,6 @@ 36: smi match: C[OH] C[OH] 36: smi match: C[CH]=O C[CH]=O 36: smi match: *=* *=* -34: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors -34: ------------------------------- -34: [09:08:13] Explicit valence for atom # 0 N, 4, is greater than permitted -34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -34: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -34: [09:08:13] WARNING: not removing hydrogen atom with dummy atom neighbors -28: ...[09:08:13] Molecule does not have explicit Hs. Consider calling AddHs() -26: done -48: Randomness seeded to: 479871284 -48: =============================================================================== -48: All tests passed (281 assertions in 10 test cases) -48: -45: [09:08:13] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [09:08:13] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -45: [09:08:13] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -45: [09:08:13] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -45: [09:08:13] non-ring atom 0 marked aromatic -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -51: Randomness seeded to: 2454161652 -51: =============================================================================== -51: All tests passed (14 assertions in 4 test cases) -51: -52: Randomness seeded to: 1320834805 -52: =============================================================================== -52: All tests passed (10 assertions in 1 test case) -52: -49: Randomness seeded to: 1826701960 -49: [09:08:13] unable to set wavy bonds for double bonds: 3 - 35/230 Test #26: testUFFForceField ...................... Passed 0.55 sec - 36/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.13 sec - 37/230 Test #51: moliteratorTestsCatch .................. Passed 0.05 sec -test 55 - Start 55: tableTestsCatch - -55: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch -55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch -56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -57: Test timeout computed to be: 1500 36: smi match: *C *C 36: smi match: C#C C#C 36: smi match: *[CH]C=C *[CH]C=C @@ -18481,6 +18772,25 @@ 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 +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.023s +2: +2: OK +45: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +72: [17:54:59] Finished: testSdf() +72: [17:54:59] ----------------------------------------- +72: +72: [17:54:59] +72: ----------------------------------------- + 43/230 Test #23: pyAlignment ............................ Passed 0.20 sec +test 85 + Start 85: v2MolSuppliers + +85: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 36: smi match: O=*C[OH] O=*C[OH] 36: smi match: *=C*=O *=C*=O 36: smi match: *=CC#N *=CC#N @@ -18496,6 +18806,34 @@ 36: smi match: c c 36: smi match: *c *c 36: smi match: *c *c +72: [17:54:59] Finished: testSmi() +72: [17:54:59] ----------------------------------------- +72: +72: [17:54:59] +72: ----------------------------------------- +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 44/230 Test #75: testTplParser .......................... Passed 0.04 sec +34: [17:54:59] WARNING: not removing hydrogen atom with dummy atom neighbors +34: ------------------------------- +34: [17:54:59] Explicit valence for atom # 0 N, 4, is greater than permitted + 45/230 Test #78: testExtendedStereoParsing .............. Passed 0.03 sec +test 86 + Start 86: v2FileParsersCatchTest + +86: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +test 87 + Start 87: multithreadedSupplierCatchTest + +87: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 36: smi match: **:*cF **:*cF 36: smi match: cB([OH])[OH] cB([OH])[OH] 36: smi match: N~N~N N~N~N @@ -18517,1281 +18855,22 @@ 36: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 36: smi match: SS SS 36: smi match: * * -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 38/230 Test #52: queryTestsCatch ........................ Passed 0.08 sec -49: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -49: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -3: static RDAny:0.061578 s -53: Randomness seeded to: 3092085464 -53: =============================================================================== -53: All tests passed (6 assertions in 1 test case) -53: - 39/230 Test #53: molbundleTestsCatch .................... Passed 0.07 sec -test 58 - Start 58: smiTest2 - -58: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -58: Test timeout computed to be: 1500 -test 59 - Start 59: cxsmilesTest - -59: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -59: Test timeout computed to be: 1500 -36: smi match: *=* *=* 36: smi match: *=* *=* 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 -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] -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 -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: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 280. -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -49: [09:08:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -49: [09:08:13] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -49: [09:08:13] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -49: =============================================================================== -49: All tests passed (2267 assertions in 79 test cases) -49: -54: Randomness seeded to: 3337174469 -54: =============================================================================== -54: All tests passed (45 assertions in 4 test cases) -54: -55: Randomness seeded to: 3594176814 -55: =============================================================================== -55: All tests passed (7 assertions in 2 test cases) -55: -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.004s -13: -13: OK -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [09:08:13] SMILES Parse Error: syntax error while parsing: - -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [09:08:13] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -58: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 40/230 Test #49: chiralityTestsCatch .................... Passed 0.12 sec - 41/230 Test #54: pickleTestsCatch ....................... Passed 0.08 sec - 42/230 Test #55: tableTestsCatch ........................ Passed 0.06 sec - 43/230 Test #58: smiTest2 ............................... Passed 0.03 sec -test 60 - Start 60: smaTest1 - -60: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -60: Test timeout computed to be: 1500 -test 61 - Start 61: smiTestCatch - -61: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -62: Test timeout computed to be: 1500 -test 63 - Start 63: v2smiTestCatch - -63: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing sf.net issue 285. -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Github2441: Add RDProps interface to Conformers. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Issue2510: Pickle Confs as double. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing loading pickled mols with conformers -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing conformer reading/writing options -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing property reading options -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing property reading options -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing boost::serialization integration -36: [09:08:13] done -36: [09:08:13] ------------------------------------- -36: [09:08:13] Testing github issue 6036 -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -56: Randomness seeded to: 2903450028 -56: =============================================================================== -56: All tests passed (72 assertions in 4 test cases) -56: -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] WARNING: not removing hydrogen atom without neighbors -57: [09:08:13] Invalid chiral specification on atom 0 -57: [09:08:13] Invalid chiral specification on atom 0 -57: [09:08:13] Invalid chiral specification on atom 0 -57: [09:08:13] Invalid chiral specification on atom 0 -57: [09:08:13] Invalid chiral specification on atom 0 -57: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -57: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' - 44/230 Test #36: graphmoltestPickler .................... Passed 0.55 sec - 45/230 Test #56: molopsTestsCatch ....................... Passed 0.12 sec -test 64 - Start 64: testDepictor - -64: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -64: Test timeout computed to be: 1500 -test 65 - Start 65: depictorCatch - -65: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -45: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [09:08:13] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 P, 7, is greater than permitted -61: Randomness seeded to: 3639760926 -61: [09:08:13] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -61: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: Randomness seeded to: 1691186716 -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry - 46/230 Test #13: pyDiscreteValueVect .................... Passed 0.78 sec -test 66 - Start 66: pyDepictor - -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-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -66: Test timeout computed to be: 1500 -45: [09:08:13] Explicit valence for atom # 0 P, 7, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 As, 7, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 As, 7, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [09:08:13] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted -45: [09:08:13] Explicit valence for atom # 1 Bi, 8, is greater than permitted -45: =============================================================================== -45: All tests passed (4464 assertions in 106 test cases) -45: -61: [09:08:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [09:08:13] SMARTS Parse Error: syntax error while parsing: C)foo -61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -61: [09:08:13] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -61: [09:08:13] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: Randomness seeded to: 14398752 -63: =============================================================================== -63: All tests passed (14 assertions in 2 test cases) -63: - 47/230 Test #45: graphmolTestsCatch ..................... Passed 0.37 sec - 48/230 Test #63: v2smiTestCatch ......................... Passed 0.08 sec -test 67 - Start 67: testMrvToMol - -67: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse -67: Test timeout computed to be: 1500 -test 68 - Start 68: fileParsersTest1 - -68: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [09:08:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -61: [09:08:13] w block attempts to set wedging on bond 0 more than once. -61: [09:08:13] improperly formatted w block -61: [09:08:13] atom 3 is not associated with bond 1(1-2) in w block -62: [09:08:13] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -62: =============================================================================== -62: All tests passed (308 assertions in 9 test cases) -62: -39: [09:08:13] sorting (hanoi sort) vectors - 49/230 Test #62: nontetrahedralCatch .................... Passed 0.16 sec -test 69 - Start 69: testAtropisomers - -69: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -69: [09:08:13] ---- Running with POSIX locale ----- -61: [09:08:13] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [09:08:13] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [09:08:13] SMARTS Parse Error: syntax error while parsing: C1C)foo -61: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -61: [09:08:13] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -61: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -61: =============================================================================== -61: All tests passed (1570 assertions in 66 test cases) -61: - 50/230 Test #61: smiTestCatch ........................... Passed 0.20 sec -test 70 - Start 70: testSquiggleDoubleBonds - -70: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -59: Randomness seeded to: 3537694454 -59: Test -59: -59: ShortAtropisomerNoCoords.cxsmi -59: -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: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: *************************************** -68: *************************************** -68: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -28: ......[09:08:13] Molecule does not have explicit Hs. Consider calling AddHs() -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -28: [09:08:13] -28: -28: **** -59: Test -59: -59: BMS-986142_atrop6.cxsmi -59: -59: Test -59: -59: BMS-986142_atropBad1.cxsmi -59: -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -28: Invariant Violation -28: bad direction in linearSearch -28: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -28: Failed Expression: status >= 0 -28: ---------- -28: Stacktrace: -28: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -28: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -28: 2# ForceFields::ForceField::minimize(unsigned int, std::vector >*, unsigned int, double, double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitForceField.so.1 -28: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/ForceField/rdForceField.so -28: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -28: 5# 0x00007FED16AB362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -28: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -28: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -28: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -28: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -28: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 11# 0x00007FED13FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 12# 0x00007FED13FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 13# 0x00007FED13FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 14# 0x00007FED13FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 15# 0x00007FED13FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -28: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so -28: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so -28: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so -28: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so -28: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -28: 21# 0x00007FED16AB03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -28: 22# _PyObject_MakeTpCall in /usr/bin/python3 -28: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 24# 0x0000000000546E76 in /usr/bin/python3 -28: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 26# _PyObject_Call_Prepend in /usr/bin/python3 -28: 27# 0x000000000059810D in /usr/bin/python3 -28: 28# 0x0000000000593E22 in /usr/bin/python3 -28: 29# _PyObject_MakeTpCall in /usr/bin/python3 -28: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 31# 0x0000000000546E76 in /usr/bin/python3 -28: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 33# _PyObject_Call_Prepend in /usr/bin/python3 -28: 34# 0x000000000059D6E4 in /usr/bin/python3 -28: 35# _PyObject_MakeTpCall in /usr/bin/python3 -28: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 37# 0x0000000000546E76 in /usr/bin/python3 -28: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 39# _PyObject_Call_Prepend in /usr/bin/python3 -28: 40# 0x000000000059D6E4 in /usr/bin/python3 -28: 41# _PyObject_MakeTpCall in /usr/bin/python3 -28: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 43# 0x0000000000546E76 in /usr/bin/python3 -28: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 45# _PyObject_Call_Prepend in /usr/bin/python3 -28: 46# 0x000000000059D6E4 in /usr/bin/python3 -28: 47# _PyObject_MakeTpCall in /usr/bin/python3 -28: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 49# _PyObject_Call_Prepend in /usr/bin/python3 -28: 50# 0x000000000059810D in /usr/bin/python3 -28: 51# 0x0000000000593E22 in /usr/bin/python3 -28: 52# _PyObject_MakeTpCall in /usr/bin/python3 -28: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 54# PyEval_EvalCode in /usr/bin/python3 -28: 55# 0x00000000005FFE7F in /usr/bin/python3 -28: 56# 0x00000000006A59F2 in /usr/bin/python3 -28: 57# _PyRun_SimpleFileObject in /usr/bin/python3 -28: 58# _PyRun_AnyFileObject in /usr/bin/python3 -28: 59# Py_RunMain in /usr/bin/python3 -28: 60# Py_BytesMain in /usr/bin/python3 -28: 61# 0x00007FED17269D68 in /lib/x86_64-linux-gnu/libc.so.6 -28: 62# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -28: 63# _start in /usr/bin/python3 -28: ---------- -28: **** -28: -60: [09:08:13] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -60: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -60: [09:08:13] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -60: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -68: [09:08:13] bond with order 0 found on line 7. This is not part of the MDL specification. -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: Test -59: -59: BMS-986142_atropBad2.cxsmi -59: -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -60: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -60: [09:08:13] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 51/230 Test #60: smaTest1 ............................... Passed 0.28 sec -test 71 - Start 71: testMolSupplier - -71: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -68: [09:08:13] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [09:08:13] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [09:08:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: Randomness seeded to: 2214421694 -70: =============================================================================== -70: All tests passed (15 assertions in 3 test cases) -70: -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 -71: [09:08:13] -71: ----------------------------------------- -68: generating smiles - 52/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.09 sec -test 72 - Start 72: testGeneralFileReader - -72: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -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 -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -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 -67: Using new chirality perception -67: Test -67: -67: rxnStereoMarkedCrossed.mrv -67: -67: Test -67: -67: NewChiralTest.sdf -67: -67: Test -67: -67: NewChiralTest.sdf -67: -67: Test -67: -67: NewChiralTestNoChiral.sdf -67: -67: Test -67: -67: NewChiralTestNoChiral.sdf -67: -67: Test -67: -67: NewChiralTestAllChiral.sdf -67: -67: Test -67: -67: NewChiralTestAllChiral.sdf -67: -67: Test -67: -67: vendor839.sdf -67: -67: Test -67: -67: ProblemShort.mol -67: -67: [09:08:13] For a MultipleSgroup expansion, the matching orphaned bond was not found -67: The multiple sgroup will be ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -65: Randomness seeded to: 2688638864 -65: =============================================================================== -65: All tests passed (577 assertions in 17 test cases) -65: -57: [09:08:13] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -57: [09:08:13] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -57: [09:08:13] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -57: [09:08:13] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -68: check isomorphism - 53/230 Test #65: depictorCatch .......................... Passed 0.25 sec -test 73 - Start 73: testMultithreadedMolSupplier - -73: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [09:08:13] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [09:08:13] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [09:08:13] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: C=c1s/c2n(c1=O)CCCCCCC\N=2 -71: [09:08:13] -71: -71: **** -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0x00007F1A56F94AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x0000562969B8B3B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x0000562969B60ADA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0x0000562969B63E0B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 7# 0x00007F1A56431D68 in /lib/x86_64-linux-gnu/libc.so.6 -71: 8# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -71: 9# 0x0000562969B659D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -72: [09:08:13] -72: ----------------------------------------- -72: [09:08:13] Finished: testDetermineFormat() -72: [09:08:13] ----------------------------------------- -72: -72: [09:08:13] -72: ----------------------------------------- -57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -57: [09:08:13] SMILES Parse Error: extra close parentheses while parsing: C) -57: [09:08:13] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 54/230 Test #57: smiTest1 ............................... Passed 0.40 sec -test 74 - Start 74: testMolWriter - -74: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] 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: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -73: [09:08:13] -73: ----------------------------------------- -34: [09:08:13] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -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: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: Test -59: -59: RP-6306_atrop6.cxsmi -59: -59: Test -59: -59: RP-6306_atropBad1.cxsmi -59: -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: Test -59: -59: RP-6306_atropBad2.cxsmi -59: -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -72: [09:08:13] Finished: testSdf() -72: [09:08:13] ----------------------------------------- -72: -72: [09:08:13] -72: ----------------------------------------- -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -28: ... -28: ---------------------------------------------------------------------- -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -3: dynamic RDAny:0.437495 s -3: static RDValue:1e-06 s -72: [09:08:13] Finished: testSmi() -72: [09:08:13] ----------------------------------------- -72: -72: [09:08:13] -72: ----------------------------------------- -28: Ran 12 tests in 0.650s -28: -28: OK -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [09:08:13] Warning: stereochemistry around double bond may be incorrect in depiction. -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: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [09:08:13] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: Test -59: -59: Sotorasib_atropBad1.cxsmi -59: -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [09:08:13] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: Test -59: -59: Sotorasib_atropBad2.cxsmi -59: -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [09:08:13] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -71: [09:08:14] Finished: testMolSup() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testRandMolSup() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -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: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [09:08:14] Finished: testSmilesSup() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ------------------------------------------------------ -71: [09:08:14] SMILES Parse Error: syntax error while parsing: fail -71: [09:08:14] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -71: [09:08:14] ERROR: Smiles parse error on line 3 -71: [09:08:14] ERROR: Cannot create molecule from : 'fail' -71: [09:08:14] ------------------------------------------------------ -71: [09:08:14] ------------------------------------------------------ -71: [09:08:14] >>> This may result in an infinite loop. It should finish almost immediately: -71: [09:08:14] <<< done. -71: [09:08:14] Finished: testSmilesSupFromText() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testSmilesWriter() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- - 55/230 Test #64: testDepictor ........................... Passed 0.53 sec -test 75 - Start 75: testTplParser - -75: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -71: [09:08:14] Finished: testSDWriter() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testSDSupplierEnding() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testSuppliersEmptyFile() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testCisTrans() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testStereoRound() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [09:08:14] Finished: testIssue226() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testTDTSupplier1() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testTDTSupplier2() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -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: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -72: [09:08:14] Finished: testMae() -72: [09:08:14] ----------------------------------------- -72: -72: [09:08:14] -72: ----------------------------------------- -71: [09:08:14] Finished: testTDTSupplier3() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testSDSupplierFromText() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Spurious data before the first property will be ignored -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Finished: testSDSupplierStrLax1() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Finished: testSDSupplierStrLax2() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Spurious data before the first property will be ignored -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Finished: testSDSupplierFromTextStrLax1() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: Problems encountered parsing data fields -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Property will be truncated after the first blank line -71: [09:08:14] Finished: testSDSupplierFromTextStrLax2() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testIssue265() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: End of data field name not found -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Explicit valence for atom # 0 F, 2, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule ending on line 16 -71: [09:08:14] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -71: [09:08:14] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] ERROR: Bond line too short: 'M END' on line 18 -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Finished: testSDErrorHandling() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -72: [09:08:14] Finished: testTdt() -72: [09:08:14] ----------------------------------------- -72: -71: [09:08:14] Finished: testIssue381() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -3: dynamic RDValue:0.080217 s -3: deleted! -3: [09:08:14] ------------------------------------- -3: [09:08:14] Testing String Pickle Roundtrips. -3: [09:08:14] done -3: [09:08:14] ------------------------------------- -3: [09:08:14] Testing conversion of vect to string. -3: [09:08:14] done -3: [09:08:14] ------------------------------------- -3: [09:08:14] Testing returning const references. -3: [09:08:14] any cast -3: [09:08:14] done: 0.001689 300000 -3: [09:08:14] copy -71: [09:08:14] Finished: testSetStreamIndices() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testMixIterAndRandom() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: build: -71: [09:08:14] Finished: testRemoveHs() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -3: [09:08:14] done: 0.001596 300000 -3: [09:08:14] ref -3: [09:08:14] done: 0.001619 300000 -3: [09:08:14] dict - 56/230 Test #72: testGeneralFileReader .................. Passed 0.34 sec -test 76 - Start 76: testMol2ToMol - -76: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -3: [09:08:14] done: 0.004615 300000 -3: [09:08:14] ref with hasVal -3: [09:08:14] done: 0.002449 300000 -3: [09:08:14] done -3: [09:08:14] ------------------------------------- -3: [09:08:14] Testing dict update. -3: [09:08:14] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -71: [09:08:14] Finished: testGetItemText() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- - 57/230 Test #28: pyForceFieldConstraints ................ Passed 1.25 sec -test 77 - Start 77: testSequence - -77: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 - 58/230 Test #3: testDict ............................... Passed 1.36 sec -test 78 - Start 78: testExtendedStereoParsing - -78: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 - 59/230 Test #75: testTplParser .......................... Passed 0.09 sec -test 79 - Start 79: fileParsersCatchTest - -79: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -71: [09:08:14] Finished: testForwardSDSupplier() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testMissingCRSDSupplier() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testIssue3482695() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] ERROR: Cannot convert 'foo' to unsigned int on line 557 -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Finished: testIssue3525673() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testBlankLinesInProps() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testSkipLines() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testGitHub23() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testGitHub88() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- - 60/230 Test #78: testExtendedStereoParsing .............. Passed 0.03 sec -test 80 - Start 80: testPropertyLists - -80: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 -71: [09:08:14] Finished: testGitHub2285() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -71: [09:08:14] ERROR: Smiles parse error on line 1 -71: [09:08:14] ERROR: Cannot create molecule from : 'c1ccccc' -71: [09:08:14] SMILES Parse Error: extra open parentheses for input: 'C(C' -71: [09:08:14] ERROR: Smiles parse error on line 3 -71: [09:08:14] ERROR: Cannot create molecule from : 'C(C' -71: [09:08:14] Explicit valence for atom # 1 C, 5, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule on line 5 -71: [09:08:14] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 -71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 -71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 -71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Atom line too short: ' -9.6' on line 28 -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Could not sanitize molecule ending on line 21 -71: [09:08:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [09:08:14] ERROR: Atom line too short: ' -9.6' on line 28 -71: [09:08:14] ERROR: moving to the beginning of the next molecule -71: [09:08:14] Finished: testGitHub2479() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0x00007F1A56F950BA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x0000562969B668CE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x0000562969B6575B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0x00007F1A56431D68 in /lib/x86_64-linux-gnu/libc.so.6 -71: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -71: 8# 0x0000562969B659D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -71: [09:08:14] Finished: testGitHub2881() -71: [09:08:14] ----------------------------------------- -71: -71: [09:08:14] ----------------------------------------- -71: [09:08:14] Finished: testGitHub3517() -71: [09:08:14] ----------------------------------------- -71: -69: Atropisomers- 1 hits 3 misses -69: Final results: -69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 61/230 Test #76: testMol2ToMol .......................... Passed 0.07 sec -test 81 - Start 81: XYZFileParserCatchTest - -81: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:54:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [17:54:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [17:54:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +34: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [17:54:59] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +34: [17:54:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [17:54:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 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 @@ -20289,13 +19368,6 @@ 77: CONECT 163 164 164 170 77: CONECT 165 166 77: CONECT 166 167 - 62/230 Test #71: testMolSupplier ........................ Passed 0.45 sec -test 82 - Start 82: cdxmlParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 77: CONECT 167 168 168 169 77: CONECT 170 171 77: CONECT 171 172 174 @@ -20783,27 +19855,99 @@ 77: CONECT 27 28 28 29 77: END 77: - 63/230 Test #69: testAtropisomers ....................... Passed 0.60 sec -79: Randomness seeded to: 4219103258 -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [09:08:14] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [09:08:14] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup 3 referenced on line 40 not found. -79: [09:08:14] +68: [17:54:59] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [17:54:59] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +68: [17:54:59] 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 +67: Using new chirality perception +67: Test +67: +67: rxnStereoMarkedCrossed.mrv +67: +67: Test +67: +67: NewChiralTest.sdf +67: +67: Test +67: +67: NewChiralTest.sdf +67: +67: Test +67: +67: NewChiralTestNoChiral.sdf +67: +67: Test +67: +67: NewChiralTestNoChiral.sdf +67: +67: Test +67: +67: NewChiralTestAllChiral.sdf +67: +67: Test +67: +67: NewChiralTestAllChiral.sdf +67: +67: Test +67: +67: vendor839.sdf +67: +67: Test +67: +67: ProblemShort.mol +67: +67: [17:54:59] For a MultipleSgroup expansion, the matching orphaned bond was not found +67: The multiple sgroup will be ignored +45: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [17:54:59] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0x00007FBD59594AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x000055D7A68703B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x000055D7A6845ADA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0x000055D7A6848E0B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 7# 0x00007FBD58A33D68 in /lib/x86_64-linux-gnu/libc.so.6 +71: 8# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +71: 9# 0x000055D7A684A9D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: +80: Randomness seeded to: 2440683067 +80: =============================================================================== +80: All tests passed (95 assertions in 4 test cases) +80: +79: Randomness seeded to: 4016343310 +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [17:54:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [17:54:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +79: [17:54:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [17:54:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +79: [17:54:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [17:54:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [17:54:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup 3 referenced on line 40 not found. +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20816,24 +19960,24 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2ADA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x0000557D532D1529 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 7# 0x000055E0E6007529 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] SGroup 3 referenced on line 40 not found. -79: [09:08:14] +79: [17:54:59] SGroup 3 referenced on line 40 not found. +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20846,29 +19990,29 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2ADA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x0000557D532D15D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 7# 0x000055E0E60075D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] no bonds -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup line too short: 'M SBV 1 6' on line 42 -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -79: [09:08:14] SGroup 2 is invalid and will be ignored -79: [09:08:14] +79: [17:54:59] no bonds +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup line too short: 'M SBV 1 6' on line 42 +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +79: [17:54:59] SGroup 2 is invalid and will be ignored +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20882,23 +20026,23 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000557D532D2192 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 8# 0x000055E0E6008192 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20912,24 +20056,24 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000557D532D223A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 8# 0x000055E0E600823A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] +79: [17:54:59] bookmark not found +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20943,25 +20087,25 @@ 79: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888DA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2ADA03E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000557D532D223A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 8# 0x000055E0E600823A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bond is not part of the SubstanceGroup -79: [09:08:14] SGroup 2 is invalid and will be ignored -79: [09:08:14] +79: [17:54:59] bond is not part of the SubstanceGroup +79: [17:54:59] SGroup 2 is invalid and will be ignored +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -20975,25 +20119,159 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000557D532D25A9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 8# 0x000055E0E60085A9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:54:59] 79: 79: **** + 46/230 Test #15: pyFPB .................................. Passed 0.23 sec + 47/230 Test #77: testSequence ........................... Passed 0.05 sec + 48/230 Test #80: testPropertyLists ...................... Passed 0.04 sec +test 88 + Start 88: testSubstructMatch + +88: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +88: Test timeout computed to be: 1500 +test 89 + Start 89: substructTestCatch + +89: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +89: Test timeout computed to be: 1500 +test 90 + Start 90: testGenericGroups + +90: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +90: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +90: Test timeout computed to be: 1500 +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 +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] +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 +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: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 280. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing sf.net issue 285. +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Github2441: Add RDProps interface to Conformers. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Issue2510: Pickle Confs as double. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing loading pickled mols with conformers +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing conformer reading/writing options +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing property reading options +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing property reading options +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing boost::serialization integration +36: [17:54:59] done +36: [17:54:59] ------------------------------------- +36: [17:54:59] Testing github issue 6036 +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:54:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [17:54:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [17:54:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +34: [17:54:59] WARNING: not removing hydrogen atom with dummy atom neighbors +68: check isomorphism +45: [17:54:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +45: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp @@ -21005,27 +20283,27 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD9ECB in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000557D532D2651 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 8# 0x000055E0E6008651 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 17# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -79: [09:08:14] SGroup 2 is invalid and will be ignored -79: [09:08:14] WARNING: final character of V3000 array is not ')' -79: [09:08:14] +79: [17:54:59] bookmark not found +79: [17:54:59] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +79: [17:54:59] SGroup 2 is invalid and will be ignored +79: [17:54:59] WARNING: final character of V3000 array is not ')' +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21043,21 +20321,21 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532CFEB3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E6005EB3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] WARNING: final character of V3000 array is not ')' -79: [09:08:14] +79: [17:54:59] WARNING: final character of V3000 array is not ')' +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21075,23 +20353,23 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532CFF4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E6005F4B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] WARNING: final character of V3000 array is not ')' -79: [09:08:14] +79: [17:54:59] bookmark not found +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] WARNING: final character of V3000 array is not ')' +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21109,21 +20387,21 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D02B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E60062B4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] WARNING: final character of V3000 array is not ')' -79: [09:08:14] +79: [17:54:59] WARNING: final character of V3000 array is not ')' +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21141,22 +20419,22 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D034C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E600634C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] SGroup 1 is invalid and will be ignored -79: [09:08:14] +79: [17:54:59] bookmark not found +79: [17:54:59] SGroup 1 is invalid and will be ignored +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21174,20 +20452,20 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D06B3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E60066B3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21205,22 +20483,22 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D074C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E600674C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] SGroup 2 is invalid and will be ignored -79: [09:08:14] +79: [17:54:59] bookmark not found +79: [17:54:59] SGroup 2 is invalid and will be ignored +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21238,20 +20516,20 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D0AB2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E6006AB2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:54:59] 79: 79: **** 79: Pre-condition Violation @@ -21269,30 +20547,229 @@ 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532D0B4C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E6006B4C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] bookmark not found -79: [09:08:14] SGroup 2 is invalid and will be ignored -79: [09:08:14] Explicit valence for atom # 2 O, 3, is greater than permitted -79: [09:08:14] Explicit valence for atom # 1 O, 3, is greater than permitted -79: [09:08:14] Explicit valence for atom # 1 C, 5, is greater than permitted -79: [09:08:14] sanitize [09:08:14] UNK: [09:08:14] 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: [09:08:14] skipping block at line 7: 'BEGIN ATOM' +79: [17:54:59] bookmark not found +79: [17:54:59] SGroup 2 is invalid and will be ignored +79: [17:54:59] Explicit valence for atom # 2 O, 3, is greater than permitted +79: [17:54:59] Explicit valence for atom # 1 O, 3, is greater than permitted +79: [17:54:59] Explicit valence for atom # 1 C, 5, is greater than permitted +81: Randomness seeded to: 449468847 +81: =============================================================================== +81: All tests passed (100 assertions in 2 test cases) +81: + 49/230 Test #81: XYZFileParserCatchTest ................. Passed 0.05 sec +60: [17:54:59] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +60: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +60: [17:54:59] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +60: [17:54:59] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +60: [17:54:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +60: [17:54:59] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 50/230 Test #76: testMol2ToMol .......................... Passed 0.07 sec +84: Randomness seeded to: 1475013493 +84: =============================================================================== +84: All tests passed (8 assertions in 1 test case) +84: + 51/230 Test #84: connectTheDotsTest ..................... Passed 0.05 sec +83: Randomness seeded to: 3768753839 +83: [17:54:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [17:54:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [17:54:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [17:54:59] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: =============================================================================== +83: All tests passed (142 assertions in 6 test cases) +83: +82: Randomness seeded to: 871330506 +82: [17:54:59] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [17:54:59] Explicit valence for atom # 3 N, 4, is greater than permitted +82: [17:54:59] CDXMLParser: failed sanitizing skipping fragment 32 +82: [17:54:59] Bad bond in CDXML skipping fragment 58... +82: [17:54:59] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [17:54:59] Bad bond in CDXML skipping fragment 58... +85: Randomness seeded to: 2346332684 +85: =============================================================================== +85: All tests passed (12 assertions in 5 test cases) +85: +86: Randomness seeded to: 3290236288 +86: =============================================================================== +86: All tests passed (6 assertions in 1 test case) +86: +59: Randomness seeded to: 1489414680 +59: Test +59: +59: ShortAtropisomerNoCoords.cxsmi +59: +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: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:54:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +26: done + 52/230 Test #26: testUFFForceField ...................... Passed 0.23 sec + 53/230 Test #60: smaTest1 ............................... Passed 0.15 sec + 54/230 Test #83: molfileStereoCatchTest ................. Passed 0.05 sec + 55/230 Test #85: v2MolSuppliers ......................... Passed 0.04 sec + 56/230 Test #86: v2FileParsersCatchTest ................. Passed 0.03 sec +test 91 + Start 91: testReaction + +91: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +91: Test timeout computed to be: 1500 +test 92 + Start 92: testReactionFingerprints + +92: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +92: Test timeout computed to be: 1500 +test 93 + Start 93: testEnumeration + +93: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +test 94 + Start 94: rxnTestCatch + +94: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +95: Test timeout computed to be: 1500 +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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +96: Test timeout computed to be: 1500 +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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +test 98 + Start 98: testChemTransforms + +98: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +98: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +98: Test timeout computed to be: 1500 + 57/230 Test #36: graphmoltestPickler .................... Passed 0.24 sec +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [17:54:59] sanitize [17:54:59] UNK: [17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [17:55:00] 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: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21304,21 +20781,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000557D532C0B3D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 3# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x000055E0E5FF6B3D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21330,45 +20807,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000557D532C0D18 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 3# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x000055E0E5FF6D18 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -81: Randomness seeded to: 929538344 -81: =============================================================================== -81: All tests passed (100 assertions in 2 test cases) -81: - 64/230 Test #77: testSequence ........................... Passed 0.14 sec - 65/230 Test #81: XYZFileParserCatchTest ................. Passed 0.08 sec -test 83 - Start 83: molfileStereoCatchTest - -83: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -test 84 - Start 84: connectTheDotsTest - -84: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21380,21 +20833,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000557D532C1151 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 3# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x000055E0E5FF7151 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21406,21 +20859,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000557D532C14D6 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 3# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x000055E0E5FF74D6 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21432,29 +20885,29 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000557D532C1753 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 3# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x000055E0E5FF7753 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 21 -79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 20 -79: [09:08:14] BEGIN SGROUP line not found on line 14 -79: [09:08:14] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -79: [09:08:14] END SGROUP line not found on line 14 -79: [09:08:14] END SGROUP line not found on line 14 -79: [09:08:14] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -79: [09:08:14] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -79: [09:08:14] +79: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 21 +79: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 20 +79: [17:55:00] BEGIN SGROUP line not found on line 14 +79: [17:55:00] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +79: [17:55:00] END SGROUP line not found on line 14 +79: [17:55:00] END SGROUP line not found on line 14 +79: [17:55:00] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +79: [17:55:00] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +79: [17:55:00] 79: 79: **** 79: Range Error @@ -21469,38 +20922,153 @@ 79: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 6# 0x0000557D5330521F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D532C6B53 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 6# 0x000055E0E603B21F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E5FFCB53 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 16# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -79: [09:08:14] Multiple ATTCHPT values for atom 2 on line 9 -79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 12 -79: [09:08:14] SMARTS Parse Error: syntax error while parsing: [#6;R -79: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -79: [09:08:14] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -79: [09:08:14] Skipping empty SMARTS value for SMARTSQ. -79: [09:08:14] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -79: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 12 -79: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -79: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [09:08:14] WARNING: Skipping property bar because the value includes an illegal blank line -79: [09:08:14] WARNING: Skipping property baz because the value includes an illegal blank line -79: [09:08:14] WARNING: Skipping property bletch +79: [17:55:00] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +79: [17:55:00] Multiple ATTCHPT values for atom 2 on line 9 +79: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [17:55:00] SMARTS Parse Error: syntax error while parsing: [#6;R +79: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +79: [17:55:00] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +79: [17:55:00] Skipping empty SMARTS value for SMARTSQ. +79: [17:55:00] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +79: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [17:55:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +59: Test +59: +59: BMS-986142_atrop6.cxsmi +59: +59: Test +59: +59: BMS-986142_atropBad1.cxsmi +59: +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: Test +59: +59: BMS-986142_atropBad2.cxsmi +59: +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [17:55:00] w block attempts to set wedging on bond 0 more than once. +61: [17:55:00] improperly formatted w block +61: [17:55:00] atom 3 is not associated with bond 1(1-2) in w block +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: [17:55:00] ------------------------------------- +88: [17:55:00] Test multithreading +88: reading molecules +19: ........... +19: ---------------------------------------------------------------------- +19: Ran 11 tests in 0.021s +19: +19: OK +19: Testing Geometry wrapper +57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +65: Randomness seeded to: 1031697384 +65: =============================================================================== +65: All tests passed (577 assertions in 17 test cases) +65: +72: [17:55:00] Finished: testMae() +72: [17:55:00] ----------------------------------------- +72: +72: [17:55:00] +72: ----------------------------------------- +72: [17:55:00] Finished: testTdt() +72: [17:55:00] ----------------------------------------- +72: +30: ...... +30: ---------------------------------------------------------------------- +30: Ran 6 tests in 0.001s +30: +30: OK +92: [17:55:00] ------------------------------------- +92: [17:55:00] Test Reaction StructuralFingerprint + 58/230 Test #2: pyCoordGen ............................. Passed 0.30 sec + 59/230 Test #65: depictorCatch .......................... Passed 0.14 sec + 60/230 Test #72: testGeneralFileReader .................. Passed 0.11 sec +test 99 + Start 99: chemTransformsTestCatch + +99: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +99: Test timeout computed to be: 1500 +test 100 + Start 100: tautomerQueryTestCatch + +100: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery +100: Test timeout computed to be: 1500 +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-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +101: Test timeout computed to be: 1500 +test 102 + Start 102: testSubgraphs1 + +102: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +102: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +102: Test timeout computed to be: 1500 +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [17:55:00] WARNING: Skipping property bar because the value includes an illegal blank line +79: [17:55:00] WARNING: Skipping property baz because the value includes an illegal blank line +79: [17:55:00] WARNING: Skipping property bletch 79: nope because the name includes a newline -79: [09:08:14] WARNING: Skipping property bletch +79: [17:55:00] WARNING: Skipping property bletch 79: nope2 because the name includes a newline -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Post-condition Violation @@ -21512,26 +21080,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888D32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x00007F76C2AC7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2AD32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532992FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E5FCF2FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Post-condition Violation @@ -21543,26 +21111,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888D32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x00007F76C2AC7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2AD32F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD47CD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532989DA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E5FCE9DA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Post-condition Violation @@ -21574,26 +21142,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x00007F76C2AC7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2AD161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D532992A4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E5FCF2A4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +79: [17:55:00] 79: 79: **** 79: Post-condition Violation @@ -21605,68 +21173,27 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x00007F6D888C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x00007F6D888D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x00007F6D888D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x00007F76C2AC7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x00007F76C2AD161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x00007F76C2AD199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# 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-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000557D53298F42 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 9# 0x000055E0E5FCEF42 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 18# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] atom 3 has a negative isotope value. line: 15 -80: Randomness seeded to: 1628274664 -80: =============================================================================== -80: All tests passed (95 assertions in 4 test cases) -80: - 66/230 Test #80: testPropertyLists ...................... Passed 0.14 sec -74: [09:08:14] 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: [09:08:14] bond with order 0 found on line 11. This is not part of the MDL specification. -74: [09:08:14] bond with order 0 found on line 16. This is not part of the MDL specification. -82: Randomness seeded to: 1667303315 -82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: [09:08:14] Explicit valence for atom # 3 N, 4, is greater than permitted -82: [09:08:14] CDXMLParser: failed sanitizing skipping fragment 32 -82: [09:08:14] Bad bond in CDXML skipping fragment 58... -82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... -test 86 - Start 86: v2FileParsersCatchTest - -86: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -79: [09:08:14] +79: [17:55:00] atom 3 has a negative isotope value. line: 15 +79: [17:55:00] 79: 79: **** 79: Invariant Violation @@ -21677,23 +21204,143 @@ 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -79: 2# 0x00007F6D88994AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 2# 0x00007F76C2B94AA4 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000557D53305604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D532DA1FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 4# 0x000055E0E603B604 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E60101FC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 14# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [09:08:14] +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] WARNING: not removing hydrogen atom without neighbors +82: [17:55:00] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +61: [17:55:00] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [17:55:00] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [17:55:00] SMARTS Parse Error: syntax error while parsing: C1C)foo +61: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +61: [17:55:00] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +61: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +61: =============================================================================== +61: All tests passed (1570 assertions in 66 test cases) +61: +88: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +88: processing +88: launch :0 +88: launch :1 +88: launch :2 +88: launch :3 +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: [17:55:00] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +57: [17:55:00] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +57: [17:55:00] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +57: [17:55:00] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +57: [17:55:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [17:55:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [17:55:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [17:55:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [17:55:00] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [17:55:00] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [17:55:00] 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 +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] ------------------------------------- +92: [17:55:00] Test Reaction DifferenceFingerprint +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +71: [17:55:00] Finished: testMolSup() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testRandMolSup() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +91: smi: O=C1CNC(=O)CN1 +91: 1: O=C1CNC(=O)CN1 +91: 2: COOC +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [17:55:00] 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 +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. +91: unmapped numbers are: 4 + 61/230 Test #61: smiTestCatch ........................... Passed 0.18 sec + 62/230 Test #92: testReactionFingerprints ............... Passed 0.05 sec +test 103 + Start 103: testSubgraphs2 + +103: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +103: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +103: Test timeout computed to be: 1500 +test 104 + Start 104: subgraphsCatch + +104: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +79: [17:55:00] 79: 79: **** 79: Pre-condition Violation @@ -21706,359 +21353,1212 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000557D532DA686 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000557D53348F68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000557D53349A88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000557D53349F00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000557D5331B783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000557D5331BAEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000557D532906BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x00007F6D87E31D68 in /lib/x86_64-linux-gnu/libc.so.6 +79: 4# 0x000055E0E6010686 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x000055E0E607EF68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x000055E0E607FA88 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x000055E0E607FF00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x000055E0E6051783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x000055E0E6051AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x000055E0E5FC66BE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x00007F76C2033D68 in /lib/x86_64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -79: 13# 0x0000557D53290701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x000055E0E5FC6701 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -82: [09:08:14] Bad bond in CDXML skipping fragment 58... - 67/230 Test #74: testMolWriter .......................... Passed 0.49 sec -test 87 - Start 87: multithreadedSupplierCatchTest - -87: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -84: Randomness seeded to: 4243776243 -84: =============================================================================== -84: All tests passed (8 assertions in 1 test case) -84: -83: Randomness seeded to: 2793746775 -83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [09:08:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: =============================================================================== -83: All tests passed (142 assertions in 6 test cases) -83: - 68/230 Test #83: molfileStereoCatchTest ................. Passed 0.08 sec - 69/230 Test #84: connectTheDotsTest ..................... Passed 0.05 sec -test 88 - Start 88: testSubstructMatch - -88: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -88: Test timeout computed to be: 1500 -test 89 - Start 89: substructTestCatch - -89: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -89: Test timeout computed to be: 1500 -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -86: Randomness seeded to: 1205933431 -86: =============================================================================== -86: All tests passed (6 assertions in 1 test case) -86: -85: Randomness seeded to: 4095904522 -85: =============================================================================== -85: All tests passed (12 assertions in 5 test cases) -85: -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: [09:08:14] ------------------------------------- -88: [09:08:14] Test multithreading -88: reading molecules - 70/230 Test #86: v2FileParsersCatchTest ................. Passed 0.06 sec -test 90 - Start 90: testGenericGroups +82: [17:55:00] Incomplete atom labelling, cannot make bond +82: [17:55:00] Incomplete atom labelling, cannot make bond +57: [17:55:00] SMILES Parse Error: extra close parentheses while parsing: C) +57: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +28: ...[17:55:00] Molecule does not have explicit Hs. Consider calling AddHs() +91: [17:55:00] atom 0 in product 0 has multiple charge specifications. +91: mass: 15.0001 +91: Oc1ccccn1 +91: Oc1ccc[nH]1 +102: ----------------------- +102: Subgraph retrieval +102: Finished +102: ----------------------- +102: testSubgraphs2a +98: 1 smi: CC +98: 1 smi: CC +98: 2 smi: CCO[C@H](N)P +98: 2 smi: CC +98: replaceSub smi1:CCP(CC)[C@@H](N)O +98: replaceSub smi1:CCNCC +98: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O +98: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O + 63/230 Test #57: smiTest1 ............................... Passed 0.22 sec +test 105 + Start 105: filterCatalogTest -90: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -90: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -90: Test timeout computed to be: 1500 -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] WARNING: not removing hydrogen atom without neighbors -82: [09:08:14] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -34: [09:08:14] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. - 71/230 Test #85: v2MolSuppliers ......................... Passed 0.10 sec -test 91 - Start 91: testReaction +105: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +105: Test timeout computed to be: 1500 +103: ----------------------- +103: Test1: pathToSubmol +45: [17:55:00] 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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +94: Randomness seeded to: 121969954 +94: [17:55:00] atom 0 in product 0 has multiple charge specifications. +102: Finished +102: ----------------------- +102: testSubgraphs2 + 64/230 Test #19: testPyGeometry ......................... Passed 0.31 sec +test 106 + Start 106: pyFilterCatalog -91: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -91: Test timeout computed to be: 1500 -82: [09:08:14] Incomplete atom labelling, cannot make bond -82: [09:08:14] Incomplete atom labelling, cannot make bond -79: [09:08:14] ERROR: molecules without atoms cannot be exported to Maestro files. -79: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -79: [09:08:14] ERROR: the mol cannot be kekulized, and will not be written to the output file. -79: [09:08:14] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -88: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -88: processing -88: launch :0 -88: launch :1 -88: launch :2 -88: launch :3 -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 -82: [09:08:14] Incomplete atom labelling, cannot make bond -79: [09:08:14] 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.[09:08:14] 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: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [09:08:14] 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: [09:08:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -34: [09:08:14] ----------------------- -34: Testing isRingFused -82: [09:08:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [09:08:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [09:08:14] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -82: [09:08:14] Failed to parse XML fragment 5 node: b attribute: Order: 5 -82: [09:08:14] Invalid or missing fragment id from CDXML fragment, assigning new one... - 72/230 Test #34: graphmolMolOpsTest ..................... Passed 1.52 sec -test 92 - Start 92: testReactionFingerprints +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-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +106: Test timeout computed to be: 1500 +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: ([C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C:2]) +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +45: [17:55:00] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: [17:55:00] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: =============================================================================== +45: All tests passed (4464 assertions in 106 test cases) +45: +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 34 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 36 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 38 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 40 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 42 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 87 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 89 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 91 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 93 +94: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 95 + 65/230 Test #30: pyDistGeom ............................. Passed 0.30 sec +test 107 + Start 107: testFragCatalog -92: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -92: Test timeout computed to be: 1500 -82: =============================================================================== -82: All tests passed (263 assertions in 7 test cases) -82: - 73/230 Test #82: cdxmlParserCatchTest ................... Passed 0.27 sec -test 93 - Start 93: testEnumeration +107: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog +107: Test timeout computed to be: 1500 +91: [17:55:00] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [17:55:00] 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: [17:55:00] reactant 2 has no mapped atoms. +91: [17:55:00] >> Atoms within one molecule have different RXN roles. +91: [17:55:00] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: ([C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +91: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +91: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +91: [17:55:00] reactant 0 has no mapped atoms. +91: [17:55:00] reactant 1 has no mapped atoms. +91: [17:55:00] reactant 3 has no mapped atoms. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 5 found multiple times. +91: [17:55:00] product atom-mapping number 6 found multiple times. +91: [17:55:00] product atom-mapping number 7 found multiple times. +91: [17:55:00] product atom-mapping number 8 found multiple times. +91: [17:55:00] product atom-mapping number 12 found multiple times. +91: [17:55:00] product atom-mapping number 9 found multiple times. +91: [17:55:00] product atom-mapping number 10 found multiple times. +91: [17:55:00] product atom-mapping number 11 found multiple times. +91: [17:55:00] reactant 0 has no mapped atoms. +91: [17:55:00] reactant 1 has no mapped atoms. +91: [17:55:00] reactant 3 has no mapped atoms. +91: [17:55:00] reactant atom-mapping number 19 found multiple times. +91: [17:55:00] reactant atom-mapping number 25 found multiple times. +91: [17:55:00] reactant atom-mapping number 20 found multiple times. +91: [17:55:00] reactant atom-mapping number 21 found multiple times. +91: [17:55:00] reactant atom-mapping number 22 found multiple times. +91: [17:55:00] reactant atom-mapping number 23 found multiple times. +91: [17:55:00] reactant atom-mapping number 24 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. + 66/230 Test #45: graphmolTestsCatch ..................... Passed 0.27 sec +94: [17:55:00] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [17:55:00] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [17:55:00] SMARTS Parse Error: unclosed ring for input: 'CC1' +94: [17:55:00] SMILES Parse Error: unclosed ring for input: 'CC1' +94: [17:55:00] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [17:55:00] product atom-mapping number 2 not found in reactants. +103: Finished +103: ----------------------- +103: Test2: Atom Environments +103: Finished +103: ----------------------- +103: Test 3: Atom Environments (Extension) +103: Finished +103: ----------------------- +103: Testing github Issue103: stereochemistry and pathToSubmol +103: Finished +103: ----------------------- +103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +103: Finished +71: [17:55:00] Finished: testSmilesSup() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ------------------------------------------------------ +71: [17:55:00] SMILES Parse Error: syntax error while parsing: fail +71: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +71: [17:55:00] ERROR: Smiles parse error on line 3 +71: [17:55:00] ERROR: Cannot create molecule from : 'fail' +71: [17:55:00] ------------------------------------------------------ +71: [17:55:00] ------------------------------------------------------ +71: [17:55:00] >>> This may result in an infinite loop. It should finish almost immediately: +71: [17:55:00] <<< done. +71: [17:55:00] Finished: testSmilesSupFromText() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSmilesWriter() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +82: [17:55:00] Incomplete atom labelling, cannot make bond +test 108 + Start 108: pyFragCatalog -93: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 -91: smi: O=C1CNC(=O)CN1 -91: 1: O=C1CNC(=O)CN1 -91: 2: COOC -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [09:08:14] 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 -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. -91: unmapped numbers are: 4 -91: [09:08:14] atom 0 in product 0 has multiple charge specifications. -91: mass: 15.0001 -92: [09:08:14] ------------------------------------- -92: [09:08:14] Test Reaction StructuralFingerprint -91: Oc1ccccn1 -91: Oc1ccc[nH]1 -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:2]) -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -91: [09:08:14] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [09:08:14] 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: [09:08:14] reactant 2 has no mapped atoms. -91: [09:08:14] >> Atoms within one molecule have different RXN roles. -91: [09:08:14] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: ([C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -91: [09:08:14] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -91: [09:08:14] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -91: [09:08:14] reactant 0 has no mapped atoms. -91: [09:08:14] reactant 1 has no mapped atoms. -91: [09:08:14] reactant 3 has no mapped atoms. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 5 found multiple times. -91: [09:08:14] product atom-mapping number 6 found multiple times. -91: [09:08:14] product atom-mapping number 7 found multiple times. -91: [09:08:14] product atom-mapping number 8 found multiple times. -91: [09:08:14] product atom-mapping number 12 found multiple times. -91: [09:08:14] product atom-mapping number 9 found multiple times. -91: [09:08:14] product atom-mapping number 10 found multiple times. -91: [09:08:14] product atom-mapping number 11 found multiple times. -91: [09:08:14] reactant 0 has no mapped atoms. -91: [09:08:14] reactant 1 has no mapped atoms. -91: [09:08:14] reactant 3 has no mapped atoms. -91: [09:08:14] reactant atom-mapping number 19 found multiple times. -91: [09:08:14] reactant atom-mapping number 25 found multiple times. -91: [09:08:14] reactant atom-mapping number 20 found multiple times. -91: [09:08:14] reactant atom-mapping number 21 found multiple times. -91: [09:08:14] reactant atom-mapping number 22 found multiple times. -91: [09:08:14] reactant atom-mapping number 23 found multiple times. -91: [09:08:14] reactant atom-mapping number 24 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. +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-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +108: Test timeout computed to be: 1500 +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 5 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 5 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 5 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 5 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 5 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 5 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 5 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 5 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)O[C@](F)(Cl)Br -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 4 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 4 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 -91: [09:08:14] product atom-mapping number 3 found multiple times. -91: [09:08:14] product atom-mapping number 2 found multiple times. -91: [09:08:14] product atom-mapping number 1 found multiple times. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. +91: [17:55:00] product atom-mapping number 3 found multiple times. +91: [17:55:00] product atom-mapping number 2 found multiple times. +91: [17:55:00] product atom-mapping number 1 found multiple times. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 -91: [09:08:14] product atom-mapping number 6 not found in reactants. -91: [09:08:14] product atom-mapping number 7 not found in reactants. -91: [09:08:14] product atom-mapping number 8 not found in reactants. -91: [09:08:14] product atom-mapping number 7 not found in reactants. -91: [09:08:14] product atom-mapping number 8 not found in reactants. -91: [09:08:14] product atom-mapping number 9 not found in reactants. -91: [09:08:14] product atom-mapping number 10 not found in reactants. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. +91: [17:55:00] product atom-mapping number 6 not found in reactants. +91: [17:55:00] product atom-mapping number 7 not found in reactants. +91: [17:55:00] product atom-mapping number 8 not found in reactants. +91: [17:55:00] product atom-mapping number 7 not found in reactants. +91: [17:55:00] product atom-mapping number 8 not found in reactants. +91: [17:55:00] product atom-mapping number 9 not found in reactants. +91: [17:55:00] product atom-mapping number 10 not found in reactants. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 -91: [09:08:14] product atom-mapping number 7 not found in reactants. -91: [09:08:14] product atom-mapping number 8 not found in reactants. -91: [09:08:14] product atom-mapping number 9 not found in reactants. -91: [09:08:14] product atom-mapping number 10 not found in reactants. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. +91: [17:55:00] product atom-mapping number 7 not found in reactants. +91: [17:55:00] product atom-mapping number 8 not found in reactants. +91: [17:55:00] product atom-mapping number 9 not found in reactants. +91: [17:55:00] product atom-mapping number 10 not found in reactants. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 -92: [09:08:14] ------------------------------------- -92: [09:08:14] Test Reaction DifferenceFingerprint -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use AtomPairGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [09:08:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator 91: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 91: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] - 74/230 Test #92: testReactionFingerprints ............... Passed 0.10 sec -test 94 - Start 94: rxnTestCatch +94: [17:55:00] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [17:55:00] product atom-mapping number 2 not found in reactants. +94: [17:55:00] CX Extensions: Substance group hierarchy is not always preserved. +94: [17:55:00] CX Extensions: Substance group hierarchy is not always preserved. +82: [17:55:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [17:55:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [17:55:00] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +82: [17:55:00] Failed to parse XML fragment 5 node: b attribute: Order: 5 +82: [17:55:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: =============================================================================== +82: All tests passed (263 assertions in 7 test cases) +82: +98: [17:55:00] SMARTS Parse Error: syntax error while parsing: bar +98: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +104: Randomness seeded to: 1518044071 +104: --------- +104: =============================================================================== +104: All tests passed (11 assertions in 1 test case) +104: +99: Randomness seeded to: 1624594517 +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000560FFCF7E256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 67/230 Test #103: testSubgraphs2 ......................... Passed 0.05 sec + 68/230 Test #104: subgraphsCatch ......................... Passed 0.04 sec +test 109 + Start 109: testDescriptors -94: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 +109: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +109: Test timeout computed to be: 1500 +test 110 + Start 110: testAUTOCORR2D + +110: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +110: Test timeout computed to be: 1500 +94: [17:55:00] reactant 0 has no mapped atoms. +94: [17:55:00] product 0 has no mapped atoms. +94: [17:55:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [17:55:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [17:55:00] Explicit valence for atom # 1 O, 5, is greater than permitted +94: =============================================================================== +94: All tests passed (702 assertions in 28 test cases) +94: + 69/230 Test #82: cdxmlParserCatchTest ................... Passed 0.17 sec +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000560FFCF7E256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000560FFCF7E256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +59: Test +59: +59: RP-6306_atrop6.cxsmi +59: +59: Test +59: +59: RP-6306_atropBad1.cxsmi +59: +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: Test +59: +59: RP-6306_atropBad2.cxsmi +59: +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +71: [17:55:00] Finished: testSDWriter() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSDSupplierEnding() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSuppliersEmptyFile() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testCisTrans() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testStereoRound() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [17:55:00] Finished: testIssue226() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testTDTSupplier1() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testTDTSupplier2() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testTDTSupplier3() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSDSupplierFromText() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Spurious data before the first property will be ignored +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Finished: testSDSupplierStrLax1() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Finished: testSDSupplierStrLax2() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Spurious data before the first property will be ignored +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Finished: testSDSupplierFromTextStrLax1() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: Problems encountered parsing data fields +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Property will be truncated after the first blank line +71: [17:55:00] Finished: testSDSupplierFromTextStrLax2() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testIssue265() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: End of data field name not found +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Explicit valence for atom # 0 F, 2, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule ending on line 16 +71: [17:55:00] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +71: [17:55:00] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] ERROR: Bond line too short: 'M END' on line 18 +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Finished: testSDErrorHandling() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testIssue381() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSetStreamIndices() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +39: [17:55:00] sorting (hanoi sort) vectors +107: 21 +79: [17:55:00] ERROR: molecules without atoms cannot be exported to Maestro files. +79: [17:55:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +79: [17:55:00] ERROR: the mol cannot be kekulized, and will not be written to the output file. +79: [17:55:00] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +79: [17:55:00] 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.[17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 70/230 Test #94: rxnTestCatch ........................... Passed 0.13 sec +test 111 + Start 111: testATF + +111: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF +111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 +test 112 + Start 112: testBCUT + +112: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +112: Test timeout computed to be: 1500 +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000560FFCF7E256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [17:55:00] Incomplete atom labelling, cannot make bond +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000560FFCF7E256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +71: [17:55:00] Finished: testMixIterAndRandom() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: build: +71: [17:55:00] Finished: testRemoveHs() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testGetItemText() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Crippen parameter acquisition. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Crippen calculation. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Issue262: problems with Crippen calculation from pickles. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test AMW calculation. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Exact MW calculation. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Labute ASA descriptors. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test TPSA descriptors. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. +91: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 + 71/230 Test #98: testChemTransforms ..................... Passed 0.13 sec +102: Finished +102: ----------------------- +102: Path retrieval +102: Finished +102: ----------------------- +102: Path retrieval2 +102: Finished +102: ----------------------- +102: Unique Subgraph retrieval +102: Finished +102: ----------------------- +102: testUniqueSubgraphs2 +110: [17:55:00] ---------------------------- +110: start test autocorr2D +69: Atropisomers- 1 hits 3 misses +69: Final results: +69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 72/230 Test #69: testAtropisomers ....................... Passed 0.25 sec +93: 30000000 30000000 +105: Warning: molecule failed filter +105: Warning: molecule failed filter: reason hzone_phenol_A(479) +105: v = { +105: 0,23}, +105: 1,22}, +105: 2,20}, +105: 3,19}, +105: 4,25}, +105: 5,24}, +105: 6,18}, +105: 7,17}, +105: 8,16}, +105: 9,21}, +105: } +105: match = { +105: 0,23}, +105: 1,22}, +105: 2,20}, +105: 3,19}, +105: 4,25}, +105: 5,24}, +105: 6,18}, +105: 7,17}, +105: 8,16}, +105: 9,21}, +105: } +105: Warning: molecule failed filter +105: Warning: molecule failed filter: reason cyano_imine_B(17) +105: v = { +105: 0,11}, +105: 1,12}, +105: 2,13}, +105: 3,14}, +105: 4,15}, +105: 5,10}, +105: 6,9}, +105: 7,8}, +105: 8,7}, +105: 9,6}, +105: 10,5}, +105: 11,17}, +105: 12,16}, +105: } +105: match = { +105: 0,11}, +105: 1,12}, +105: 2,13}, +105: 3,14}, +105: 4,15}, +105: 5,10}, +105: 6,9}, +105: 7,8}, +105: 8,7}, +105: 9,6}, +105: 10,5}, +105: 11,17}, +105: 12,16}, +105: } +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: } +test 113 + Start 113: testEEM + +113: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM +113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +test 114 + Start 114: testPBF + +114: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF +114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +99: [17:55:00] +99: +99: **** +99: Invariant Violation +99: molzip: zipped Bond already exists, perhaps labels are duplicated +99: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 5# 0x0000560FFCF7343D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000560FFCFCFE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000560FFCFD0988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000560FFCFD0E00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000560FFCFA2783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000560FFCFA2AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000560FFCF7263E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 12# 0x00007FB8EA833D68 in /lib/x86_64-linux-gnu/libc.so.6 +99: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +99: 14# 0x0000560FFCF72681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: =============================================================================== +99: All tests passed (674 assertions in 9 test cases) +99: +71: [17:55:00] Finished: testForwardSDSupplier() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testMissingCRSDSupplier() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testIssue3482695() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] ERROR: Cannot convert 'foo' to unsigned int on line 557 +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Finished: testIssue3525673() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testBlankLinesInProps() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testSkipLines() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testGitHub23() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testGitHub88() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +91: [17:55:00] product atom-mapping number 17 not found in reactants. +91: [17:55:00] product atom-mapping number 18 not found in reactants. +91: [17:55:00] mapped atoms in the reactants were not mapped in the products. +91: unmapped numbers are: 12 +3: dynamic boost any:0.362374 s + 73/230 Test #99: chemTransformsTestCatch ................ Passed 0.14 sec +test 115 + Start 115: testRDFcustom + +115: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +71: [17:55:00] Finished: testGitHub2285() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +71: [17:55:00] ERROR: Smiles parse error on line 1 +71: [17:55:00] ERROR: Cannot create molecule from : 'c1ccccc' +71: [17:55:00] SMILES Parse Error: extra open parentheses for input: 'C(C' +71: [17:55:00] ERROR: Smiles parse error on line 3 +71: [17:55:00] ERROR: Cannot create molecule from : 'C(C' +71: [17:55:00] Explicit valence for atom # 1 C, 5, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule on line 5 +71: [17:55:00] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +71: [17:55:00] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule ending on line 21 +71: [17:55:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule ending on line 21 +71: [17:55:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule ending on line 21 +71: [17:55:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Atom line too short: ' -9.6' on line 28 +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Could not sanitize molecule ending on line 21 +71: [17:55:00] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [17:55:00] ERROR: Atom line too short: ' -9.6' on line 28 +71: [17:55:00] ERROR: moving to the beginning of the next molecule +71: [17:55:00] Finished: testGitHub2479() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0x00007FBD595950BA in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x000055D7A684B8CE in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x000055D7A684A75B in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0x00007FBD58A33D68 in /lib/x86_64-linux-gnu/libc.so.6 +71: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +71: 8# 0x000055D7A684A9D1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: +71: [17:55:00] Finished: testGitHub2881() +71: [17:55:00] ----------------------------------------- +71: +71: [17:55:00] ----------------------------------------- +71: [17:55:00] Finished: testGitHub3517() +71: [17:55:00] ----------------------------------------- +71: +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: Test +59: +59: Sotorasib_atropBad1.cxsmi +59: +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: Test +59: +59: Sotorasib_atropBad2.cxsmi +59: +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +112: [17:55:00] ------------------------------------- +112: [17:55:00] Basic BCUT tests. +88: done +88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +88: processing2 +88: launch2 :0 +88: launch2 :1 +88: launch2 :2 +88: launch2 :3 + 74/230 Test #111: testATF ................................ Passed 0.04 sec +test 116 + Start 116: testRDF + +116: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 + 75/230 Test #71: testMolSupplier ........................ Passed 0.27 sec +test 117 + Start 117: testMORSE + +117: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Lipinski parameters. +113: =>start test EEM +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 0 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [17:55:00] done +112: [17:55:00] ------------------------------------- +112: [17:55:00] Larger BCUT tests. +114: [17:55:00] ------------------------------------- +114: [17:55:00] Basic PBF tests. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +74: [17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [17:55:00] Warning: stereochemistry around double bond may be incorrect in depiction. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +74: [17:55:00] bond with order 0 found on line 11. This is not part of the MDL specification. +74: [17:55:00] bond with order 0 found on line 16. This is not part of the MDL specification. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: done +88: preprocessing 3 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +88: processing3 +88: launch3 :0 +88: launch3 :1 +88: launch3 :2 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: launch3 :3 +3: static RDAny:0.04949 s +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: [17:55:00] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +91: [17:55:00] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +91: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: [17:55:00] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: ------------- +91: CCOc1ccccc1 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 76/230 Test #74: testMolWriter .......................... Passed 0.31 sec +test 118 + Start 118: test3D + +118: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D +118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: [17:55:00] ------------------------------------- +118: [17:55:00] Basic PMI tests. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: Randomness seeded to: 2706064596 +100: =============================================================================== +100: All tests passed (93 assertions in 13 test cases) +100: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: badWedgeError.sdf @@ -22371,10 +22871,62 @@ 67: 67: MulticenterSgroup.mrv 67: -67: [09:08:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -67: [09:08:14] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. -91: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +67: [17:55:00] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +67: [17:55:00] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 77/230 Test #100: tautomerQueryTestCatch ................. Passed 0.23 sec +test 119 + Start 119: testWHIM + +119: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM +119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: GenericSgroup.mrv @@ -22407,7 +22959,7 @@ 67: 67: MarvinBadMissingMolID.mrv 67: -67: [09:08:14] +67: [17:55:00] 67: 67: **** 67: Test Assert @@ -22418,12 +22970,12 @@ 67: Stacktrace: 67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 2# 0x00005632600C099F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 3# 0x00005632600CB5EC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 4# 0x00005632600B8A5D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 5# 0x00007F6701231D68 in /lib/x86_64-linux-gnu/libc.so.6 +67: 2# 0x000055EBC35FD99F in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 3# 0x000055EBC36085EC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 4# 0x000055EBC35F5A5D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 5# 0x00007F1F1C033D68 in /lib/x86_64-linux-gnu/libc.so.6 67: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -67: 7# 0x00005632600B8BE1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 7# 0x000055EBC35F5BE1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: ---------- 67: **** 67: @@ -22441,16 +22993,23 @@ 67: 67: MarvinBadY2.mrv 67: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: The values x2 and y2 must be large floats in MRV file 67: Test 67: 67: MarvinBadStereoGroupsAbs.mrv 67: 67: Unrecognized group definition -91: [09:08:14] product atom-mapping number 17 not found in reactants. -91: [09:08:14] product atom-mapping number 18 not found in reactants. -91: [09:08:14] mapped atoms in the reactants were not mapped in the products. -91: unmapped numbers are: 12 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 78/230 Test #64: testDepictor ........................... Passed 0.40 sec +test 120 + Start 120: testGETAWAY + +120: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +120: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadElementType.mrv @@ -22506,22 +23065,30 @@ 67: 67: MarvinBadSruAtomRef.mrv 67: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadSruAtomRef.mrv 67: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadSruConnect.mrv 67: 67: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadSupAttachBond.mrv @@ -22532,60 +23099,784 @@ 67: MarvinBadSupAttachOrder.mrv 67: 67: Order for an AttachmentPoint definition must be an integer in MRV file +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadSupMissingAttachBond.mrv 67: 67: No attachment point found for bond to the condensed atom in a superatomSgroup +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: MarvinBadSupMissingAttachOrder.mrv 67: 67: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -66: ..............[09:08:14] SMILES Parse Error: syntax error while parsing: invalidsmiles -66: [09:08:14] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -88: done -88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -88: processing2 -88: launch2 :0 -88: launch2 :1 -88: launch2 :2 -88: launch2 :3 +113: 100 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +28: ......[17:55:00] Molecule does not have explicit Hs. Consider calling AddHs() +28: [17:55:00] +28: +28: **** 88: done -88: preprocessing 3 -88: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -88: processing3 -88: launch3 :0 -88: launch3 :1 -88: launch3 :2 -88: launch3 :3 -94: Randomness seeded to: 3114013220 -94: [09:08:14] atom 0 in product 0 has multiple charge specifications. -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 34 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 36 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 38 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 40 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 42 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 87 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 89 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 91 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 93 -94: [09:08:14] Found a SCD/SED line with missing/empty SDT specification at line 95 +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test GitHub issue 15 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test VSA descriptors. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: [17:55:00] done +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test GitHub issue 409 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test molecular formula calculation. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Issue 3415534. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test Issue3433771: Bad definition for Crippen atom type O11. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +28: Invariant Violation +28: bad direction in linearSearch +28: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +28: Failed Expression: status >= 0 +28: ---------- +28: Stacktrace: +28: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +28: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +28: 2# ForceFields::ForceField::minimize(unsigned int, std::vector >*, unsigned int, double, double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitForceField.so.1 +28: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/ForceField/rdForceField.so +28: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +28: 5# 0x00007FDDBE1EB62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +28: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +28: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +28: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +28: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +28: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 11# 0x00007FDDBB7AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 12# 0x00007FDDBB7AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 13# 0x00007FDDBB7AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 14# 0x00007FDDBB7AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 15# 0x00007FDDBB7AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +28: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so +28: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so +28: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so +28: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so +28: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +28: 21# 0x00007FDDBE1E83C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +28: 22# _PyObject_MakeTpCall in /usr/bin/python3 +28: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 24# 0x0000000000546E76 in /usr/bin/python3 +28: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 26# _PyObject_Call_Prepend in /usr/bin/python3 +28: 27# 0x000000000059810D in /usr/bin/python3 +28: 28# 0x0000000000593E22 in /usr/bin/python3 +28: 29# _PyObject_MakeTpCall in /usr/bin/python3 +28: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 31# 0x0000000000546E76 in /usr/bin/python3 +28: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 33# _PyObject_Call_Prepend in /usr/bin/python3 +28: 34# 0x000000000059D6E4 in /usr/bin/python3 +28: 35# _PyObject_MakeTpCall in /usr/bin/python3 +28: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 37# 0x0000000000546E76 in /usr/bin/python3 +28: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 39# _PyObject_Call_Prepend in /usr/bin/python3 +28: 40# 0x000000000059D6E4 in /usr/bin/python3 +28: 41# _PyObject_MakeTpCall in /usr/bin/python3 +28: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 43# 0x0000000000546E76 in /usr/bin/python3 +28: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 45# _PyObject_Call_Prepend in /usr/bin/python3 +28: 46# 0x000000000059D6E4 in /usr/bin/python3 +28: 47# _PyObject_MakeTpCall in /usr/bin/python3 +28: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 49# _PyObject_Call_Prepend in /usr/bin/python3 +28: 50# 0x000000000059810D in /usr/bin/python3 +28: 51# 0x0000000000593E22 in /usr/bin/python3 +28: 52# _PyObject_MakeTpCall in /usr/bin/python3 +28: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 54# PyEval_EvalCode in /usr/bin/python3 +28: 55# 0x00000000005FFE7F in /usr/bin/python3 +28: 56# 0x00000000006A59F2 in /usr/bin/python3 +28: 57# _PyRun_SimpleFileObject in /usr/bin/python3 +28: 58# _PyRun_AnyFileObject in /usr/bin/python3 +28: 59# Py_RunMain in /usr/bin/python3 +28: 60# Py_BytesMain in /usr/bin/python3 +28: 61# 0x00007FDDBE993D68 in /lib/x86_64-linux-gnu/libc.so.6 +28: 62# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +28: 63# _start in /usr/bin/python3 +28: ---------- +28: **** +28: +109: [17:55:00] done +109: [17:55:00] ------------------------------------- +109: [17:55:00] Test multithreading +109: reading molecules +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102: Finished +102: ----------------------- +102: testRootedSubgraphs +102: Finished +102: ----------------------- +102: testRootedPaths +102: Finished +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test chiral matching + 79/230 Test #105: filterCatalogTest ...................... Passed 0.27 sec +test 121 + Start 121: testAUTOCORR3D + +121: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +121: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test dative-bond matching +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test cis/trans matching +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test cis/trans matching part 2 +88: [17:55:00] done +88: [17:55:00] ------------------------------------- +88: [17:55:00] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +88: [17:55:00] done +96: [17:55:00] == testCartesianProduct +89: Randomness seeded to: 3645777251 +89: =============================================================================== +89: All tests passed (197 assertions in 9 test cases) +89: + 80/230 Test #89: substructTestCatch ..................... Passed 0.36 sec + 81/230 Test #102: testSubgraphs1 ......................... Passed 0.30 sec +test 122 + Start 122: testCoulombMat + +122: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +122: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +122: Test timeout computed to be: 1500 +test 123 + Start 123: descriptorsTestCatch + +123: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +123: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +123: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +88: [17:55:00] ------------------------------------- +88: [17:55:00] Testing matching E/Z against Cis/Trans stereo bonds +88: [17:55:00] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 4# 0x000055A05E9CA536 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x000055A05E9C7C21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0x00007F35BDA33D68 in /lib/x86_64-linux-gnu/libc.so.6 +88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +88: 8# 0x000055A05E9C7D61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: ---------- +88: **** +88: +88: [17:55:00] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +88: 4# 0x000055A05E9BDCF9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x000055A05E9C7C21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0x00007F35BDA33D68 in /lib/x86_64-linux-gnu/libc.so.6 +88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +88: 8# 0x000055A05E9C7D61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: ---------- +88: **** +88: +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test substructure matching with a pathological case for symmetric SSSR +88: [17:55:00] ------------------------------------- +88: [17:55:00] Test isAtomTerminalRGroupOrQueryHydrogen +96: .[17:55:00] == testEnumerateLibrary +97: .[17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. + 82/230 Test #88: testSubstructMatch ..................... Passed 0.38 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +124: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +96: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +96: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +96: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: .[17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: () +97: ******************************************** +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 [*:1] +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M RGP 1 1 2 +97: V 1 [*:2] +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 1 2 1 0 +97: M RGP 2 1 1 2 2 +97: V 1 [*:1] +97: V 2 [*:2] +97: M END +97: +97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 [*:1] +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M RGP 1 1 2 +97: V 1 [*:2] +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 1 2 1 0 +97: M RGP 2 1 1 2 2 +97: V 1 [*:1] +97: V 2 [*:2] +97: M END +97: +97: ******************************************** +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 * +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M RGP 1 1 2 +97: V 1 * +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M RGP 2 1 1 2 2 +97: V 1 * +97: V 2 * +97: M END +97: +97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 [*:1] +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M RGP 1 1 2 +97: V 1 [*:2] +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 1 2 1 0 +97: M RGP 2 1 1 2 2 +97: V 1 [*:1] +97: V 2 [*:2] +97: M END +97: +97: ******************************************** +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M ISO 1 2 1 +97: V 1 halogen.bromine.aromatic +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M ISO 1 1 2 +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M ISO 2 1 1 2 2 +97: M END +97: +97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 [*:1] +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M RGP 1 1 2 +97: V 1 [*:2] +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +97: 1 2 1 0 +97: M RGP 2 1 1 2 2 +97: V 1 [*:1] +97: V 2 [*:2] +97: M END +97: +97: ******************************************** +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M ISO 1 2 1 +97: V 1 halogen.bromine.aromatic +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M ISO 1 1 3 +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M ISO 2 1 1 2 2 +97: M END +97: [17:55:00] reactant 0 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] product 0 has no mapped atoms. +97: [17:55:00] Could not find RLabel mapping for atom: 0 in template: 1 +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: [17:55:00] reactant 1 has no mapped atoms. +97: .. +97: ---------------------------------------------------------------------- +97: Ran 4 tests in 0.023s +97: +97: OK +97: +97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +97: $RXN +97: +97: RDKit +97: +97: 2 1 +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 1 0 0 0 0 0 0999 V2000 +97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 1 2 1 0 +97: M RGP 1 2 1 +97: V 1 halogen.bromine.aromatic +97: V 2 [*:1] +97: M STY 1 1 DAT +97: M SAL 1 1 1 +97: M SED 1 [#35&$([Br&$(Br-&!@c)])] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 4 3 0 1 0 0 0 0 0 0999 V2000 +97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +97: 2 3 1 0 +97: 1 2 1 0 +97: 2 4 1 0 +97: M ISO 1 1 3 +97: V 2 boronicacid +97: M STY 1 1 DAT +97: M SAL 1 1 2 +97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +97: M END +97: $MOL +97: +97: RDKit 2D +97: +97: 2 1 0 0 0 0 0 0 0 0999 V2000 +97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +97: 1 2 1 0 +97: M ISO 1 2 2 +97: M RGP 1 1 1 +97: V 1 [*:1] +97: M END +97: +97: $RXN Failed +109: processing +109: launch :0 +109: launch :1 +109: launch :2 +109: launch :3 67: Test 67: 67: marvin03.mrv @@ -22650,686 +23941,21 @@ 67: 67: BMS-986142_atrop5.mrv 67: -67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -94: [09:08:14] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [09:08:14] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [09:08:14] SMARTS Parse Error: unclosed ring for input: 'CC1' -94: [09:08:14] SMILES Parse Error: unclosed ring for input: 'CC1' -91: [09:08:14] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -91: [09:08:14] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -91: -94: [09:08:14] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [09:08:14] product atom-mapping number 2 not found in reactants. -94: [09:08:14] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [09:08:14] product atom-mapping number 2 not found in reactants. -91: [09:08:14] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -91: ------------- -91: CCOc1ccccc1 -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: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -94: [09:08:14] CX Extensions: Substance group hierarchy is not always preserved. -94: [09:08:14] CX Extensions: Substance group hierarchy is not always preserved. -67: Test -67: -67: BMS-986142_atropBad2.mrv -67: -67: [09:08:14] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -93: 30000000 30000000 -94: [09:08:14] reactant 0 has no mapped atoms. -94: [09:08:14] product 0 has no mapped atoms. -94: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [09:08:14] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [09:08:14] Explicit valence for atom # 1 O, 5, is greater than permitted -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: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -94: =============================================================================== -94: All tests passed (702 assertions in 28 test cases) -94: - 75/230 Test #94: rxnTestCatch ........................... Passed 0.26 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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -95: Test timeout computed to be: 1500 -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: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: Test -67: -67: RP-6306_atropBad1.mrv -67: -67: [09:08:14] 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: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:14] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:14] 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: [09:08:14] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0x00007FE02B6C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0x00007FE02B6D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# 0x00007FE02B6D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 6# 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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 9# 0x0000556B52AD1CF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x0000556B52B384F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0x0000556B52AB8963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 12# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 14# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -88: done -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test GitHub issue 15 -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test GitHub issue 409 -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test chiral matching -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test dative-bond matching -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test cis/trans matching -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test cis/trans matching part 2 -88: [09:08:14] done -88: [09:08:14] ------------------------------------- -88: [09:08:14] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -88: [09:08:14] done -89: Randomness seeded to: 3891049858 -89: =============================================================================== -89: All tests passed (197 assertions in 9 test cases) -89: -88: [09:08:14] ------------------------------------- -88: [09:08:14] Testing matching E/Z against Cis/Trans stereo bonds -88: [09:08:14] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x000055E860EFE536 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x000055E860EFBC21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0x00007F647A031D68 in /lib/x86_64-linux-gnu/libc.so.6 -88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -88: 8# 0x000055E860EFBD61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: ---------- -88: **** -88: -88: [09:08:14] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x000055E860EF1CF9 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x000055E860EFBC21 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0x00007F647A031D68 in /lib/x86_64-linux-gnu/libc.so.6 -88: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -88: 8# 0x000055E860EFBD61 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: ---------- -88: **** -88: -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test substructure matching with a pathological case for symmetric SSSR - 76/230 Test #89: substructTestCatch ..................... Passed 0.58 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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -96: Test timeout computed to be: 1500 -88: [09:08:14] ------------------------------------- -88: [09:08:14] Test isAtomTerminalRGroupOrQueryHydrogen -66: ..... -66: ---------------------------------------------------------------------- -66: Ran 19 tests in 0.750s -66: -66: OK - 77/230 Test #88: testSubstructMatch ..................... Passed 0.60 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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -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: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: Test -67: -67: Sotorasib_atropBad1.mrv -67: -67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -91: [09:08:15] reactant 0 has no mapped atoms. -91: [09:08:15] product 0 has no mapped atoms. -91: [09:08:15] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -67: Test -67: -67: Sotorasib_atropBad2.mrv -67: -67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 - 78/230 Test #91: testReaction ........................... Passed 0.63 sec -test 98 - Start 98: testChemTransforms - -98: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -98: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -98: Test timeout computed to be: 1500 -98: 1 smi: CC -98: 1 smi: CC -98: 2 smi: CCO[C@H](N)P -98: 2 smi: CC -98: replaceSub smi1:CCP(CC)[C@@H](N)O -98: replaceSub smi1:CCNCC -98: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O -98: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -98: [09:08:15] SMARTS Parse Error: syntax error while parsing: bar -98: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -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: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -68: [09:08:15] 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: [09:08:15] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. - 79/230 Test #98: testChemTransforms ..................... Passed 0.11 sec -test 99 - Start 99: chemTransformsTestCatch - -99: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -99: Test timeout computed to be: 1500 -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: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 - 80/230 Test #66: pyDepictor ............................. Passed 1.59 sec -test 100 - Start 100: tautomerQueryTestCatch - -100: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery -100: Test timeout computed to be: 1500 -68: ---------------------------------- -68: ---------------------------------- -68: [09:08:15] -68: -68: **** -99: Randomness seeded to: 1545041524 -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] -99: -99: **** -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x0000556B52ADF0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x0000556B52B3856A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x0000556B52AB8963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 8# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -68: [09:08:15] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -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: All tests passed (2445 assertions in 29 test cases) -59: -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: - 81/230 Test #59: cxsmilesTest ........................... Passed 1.76 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-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -101: Test timeout computed to be: 1500 -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [09:08:15] Incomplete atom labelling, cannot make bond -99: [09:08:15] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x000055E87A3ED256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [09:08:15] -99: -99: **** -99: Invariant Violation -99: molzip: zipped Bond already exists, perhaps labels are duplicated -99: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-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-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 5# 0x000055E87A3E243D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x000055E87A43EE68 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x000055E87A43F988 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x000055E87A43FE00 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x000055E87A411783 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x000055E87A411AEC in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x000055E87A3E163E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 12# 0x00007F4815431D68 in /lib/x86_64-linux-gnu/libc.so.6 -99: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -99: 14# 0x000055E87A3E1681 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: =============================================================================== -99: All tests passed (674 assertions in 9 test cases) -99: - 82/230 Test #99: chemTransformsTestCatch ................ Passed 0.14 sec -test 102 - Start 102: testSubgraphs1 - -102: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -102: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -102: Test timeout computed to be: 1500 -102: ----------------------- -102: Subgraph retrieval -102: Finished -102: ----------------------- -102: testSubgraphs2a -102: Finished -102: ----------------------- -102: testSubgraphs2 -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: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -102: Finished -102: ----------------------- -102: Path retrieval -102: Finished -102: ----------------------- -102: Path retrieval2 -102: Finished -102: ----------------------- -102: Unique Subgraph retrieval -102: Finished -102: ----------------------- -102: testUniqueSubgraphs2 -95: ...[09:08:15] +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101: ..... +101: ---------------------------------------------------------------------- +101: Ran 5 tests in 0.046s +101: +101: OK +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +95: ...[17:55:00] 95: 95: **** -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: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 95: Pre-condition Violation 95: getNumImplicitHs() called without preceding call to calcImplicitValence() 95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp @@ -23361,7 +23987,7 @@ 95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -95: 25# 0x00007FA463A4B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +95: 25# 0x00007F2C2295C62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 27# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 95: 28# 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23372,17 +23998,17 @@ 95: 33# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 34# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 95: 35# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 36# 0x00007FA460FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 37# 0x00007FA460FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 38# 0x00007FA460FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 39# 0x00007FA460FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 40# 0x00007FA460FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 36# 0x00007F2C1FFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 37# 0x00007F2C1FFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 38# 0x00007F2C1FFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 39# 0x00007F2C1FFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 40# 0x00007F2C1FFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 41# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 42# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 43# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 44# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -95: 46# 0x00007FA463A483C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +95: 46# 0x00007F2C229593C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 47# _PyObject_MakeTpCall in /usr/bin/python3 95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 49# 0x0000000000546E76 in /usr/bin/python3 @@ -23415,20 +24041,19 @@ 95: 76# _PyRun_AnyFileObject in /usr/bin/python3 95: 77# Py_RunMain in /usr/bin/python3 95: 78# Py_BytesMain in /usr/bin/python3 -95: 79# 0x00007FA464391D68 in /lib/x86_64-linux-gnu/libc.so.6 +95: 79# 0x00007F2C23283D68 in /lib/x86_64-linux-gnu/libc.so.6 95: 80# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 95: 81# _start in /usr/bin/python3 95: ---------- 95: **** 95: -95: [09:08:15] +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +95: [17:55:00] 95: 95: **** -67: Test -67: -67: BMS-986142_atropBad2.mrv -67: -67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 95: Pre-condition Violation 95: getNumImplicitHs() called without preceding call to calcImplicitValence() 95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp @@ -23460,7 +24085,7 @@ 95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -95: 25# 0x00007FA463A4B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +95: 25# 0x00007F2C2295C62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 27# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 95: 28# 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23471,17 +24096,17 @@ 95: 33# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 95: 34# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 95: 35# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 36# 0x00007FA460FAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 37# 0x00007FA460FAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 38# 0x00007FA460FAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 39# 0x00007FA460FAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -95: 40# 0x00007FA460FAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 36# 0x00007F2C1FFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 37# 0x00007F2C1FFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 38# 0x00007F2C1FFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 39# 0x00007F2C1FFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +95: 40# 0x00007F2C1FFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 95: 41# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 42# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 43# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 44# 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-x86_64-linux-gnu/rdkit/rdBase.so 95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -95: 46# 0x00007FA463A483C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +95: 46# 0x00007F2C229593C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 95: 47# _PyObject_MakeTpCall in /usr/bin/python3 95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 95: 49# 0x0000000000546E76 in /usr/bin/python3 @@ -23514,2059 +24139,228 @@ 95: 76# _PyRun_AnyFileObject in /usr/bin/python3 95: 77# Py_RunMain in /usr/bin/python3 95: 78# Py_BytesMain in /usr/bin/python3 -95: 79# 0x00007FA464391D68 in /lib/x86_64-linux-gnu/libc.so.6 +95: 79# 0x00007F2C23283D68 in /lib/x86_64-linux-gnu/libc.so.6 95: 80# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 95: 81# _start in /usr/bin/python3 95: ---------- 95: **** 95: -90: Randomness seeded to: 1813137230 -90: =============================================================================== -90: All tests passed (11480 assertions in 38 test cases) -90: - 83/230 Test #90: testGenericGroups ...................... Passed 1.07 sec -test 103 - Start 103: testSubgraphs2 - -103: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -103: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -103: Test timeout computed to be: 1500 -95: .........[09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [09:08:15] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: .[09:08:15] product atom-mapping number 1 found multiple times. -95: [09:08:15] product atom-mapping number 1 found multiple times. -100: Randomness seeded to: 1851626409 -100: =============================================================================== -100: All tests passed (93 assertions in 13 test cases) -100: - 84/230 Test #100: tautomerQueryTestCatch ................. Passed 0.29 sec -test 104 - Start 104: subgraphsCatch - -104: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 -95: ................[09:08:15] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 3 -95: [09:08:15] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 3 -67: Test -67: -67: JDQ443_3d.mrv -67: +113: [17:55:00] 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_atrop1.mrv +67: BMS-986142_atrop6.mrv 67: 67: Test 67: -67: JDQ443_atrop2.mrv +67: BMS-986142_atrop7.mrv 67: 67: Test 67: -67: JDQ443_atrop3.mrv +67: BMS-986142_atrop8.mrv 67: +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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_atropBad1.mrv +67: BMS-986142_atropBad2.mrv 67: -67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -97: .[09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -103: ----------------------- -103: Test1: pathToSubmol -97: .[09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -95: .[09:08:15] mapped atoms in the reactants were not mapped in the products. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +122: ===================== Testing CoulombMat ======================= +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +95: .........[17:55:00] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [17:55:00] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [17:55:00] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [17:55:00] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +34: [17:55:00] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +95: .[17:55:00] product atom-mapping number 1 found multiple times. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +95: [17:55:00] product atom-mapping number 1 found multiple times. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +122: CM test 1 mat Done + 83/230 Test #122: testCoulombMat ......................... Passed 0.06 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +125: Test timeout computed to be: 1500 +95: ................[17:55:00] mapped atoms in the reactants were not mapped in the products. 95: unmapped numbers are: 3 -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: () -97: ******************************************** -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 [*:1] -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M RGP 1 1 2 -97: V 1 [*:2] -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 1 2 1 0 -97: M RGP 2 1 1 2 2 -97: V 1 [*:1] -97: V 2 [*:2] -97: M END -97: -97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 [*:1] -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M RGP 1 1 2 -97: V 1 [*:2] -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 1 2 1 0 -97: M RGP 2 1 1 2 2 -97: V 1 [*:1] -97: V 2 [*:2] -97: M END -97: -97: ******************************************** -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 * -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M RGP 1 1 2 -97: V 1 * -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M RGP 2 1 1 2 2 -97: V 1 * -97: V 2 * -97: M END -97: -97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 [*:1] -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M RGP 1 1 2 -97: V 1 [*:2] -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 1 2 1 0 -97: M RGP 2 1 1 2 2 -97: V 1 [*:1] -97: V 2 [*:2] -97: M END -97: -97: ******************************************** -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M ISO 1 2 1 -97: V 1 halogen.bromine.aromatic -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M ISO 1 1 2 -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M ISO 2 1 1 2 2 -97: M END -97: -97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 [*:1] -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M RGP 1 1 2 -97: V 1 [*:2] -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -97: 1 2 1 0 -97: M RGP 2 1 1 2 2 -97: V 1 [*:1] -97: V 2 [*:2] -97: M END -97: -97: ******************************************** -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M ISO 1 2 1 -97: V 1 halogen.bromine.aromatic -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M ISO 1 1 3 -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M ISO 2 1 1 2 2 -97: M END -97: [09:08:15] reactant 0 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] product 0 has no mapped atoms. -97: [09:08:15] Could not find RLabel mapping for atom: 0 in template: 1 -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -97: [09:08:15] reactant 1 has no mapped atoms. -67: Test -67: -67: RP-6306_atrop1.mrv -67: -67: Test -67: -67: RP-6306_atrop2.mrv -67: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: [17:55:00] reactant 0 has no mapped atoms. +91: [17:55:00] product 0 has no mapped atoms. +91: [17:55:00] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +95: [17:55:00] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 3 +95: .[17:55:00] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 3 +96: ..[17:55:00] == testRGroupState 67: Test 67: -67: RP-6306_atrop3.mrv +67: JDQ443_3d.mrv 67: 67: Test 67: -67: RP-6306_atrop4.mrv +67: JDQ443_atrop1.mrv 67: 67: Test 67: -67: RP-6306_atrop5.mrv +67: JDQ443_atrop2.mrv 67: -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -97: .. -97: ---------------------------------------------------------------------- -97: Ran 4 tests in 0.028s -97: -97: OK -97: -97: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -97: $RXN -97: -97: RDKit -97: -97: 2 1 -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 1 0 0 0 0 0 0999 V2000 -97: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -97: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 1 2 1 0 -97: M RGP 1 2 1 -97: V 1 halogen.bromine.aromatic -97: V 2 [*:1] -97: M STY 1 1 DAT -97: M SAL 1 1 1 -97: M SED 1 [#35&$([Br&$(Br-&!@c)])] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 4 3 0 1 0 0 0 0 0 0999 V2000 -97: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -97: 2 3 1 0 -97: 1 2 1 0 -97: 2 4 1 0 -97: M ISO 1 1 3 -97: V 2 boronicacid -97: M STY 1 1 DAT -97: M SAL 1 1 2 -97: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -97: M END -97: $MOL -97: -97: RDKit 2D -97: -97: 2 1 0 0 0 0 0 0 0 0999 V2000 -97: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -97: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -97: 1 2 1 0 -97: M ISO 1 2 2 -97: M RGP 1 1 1 -97: V 1 [*:1] -97: M END -97: -97: $RXN Failed 67: Test 67: -67: RP-6306_atropBad1.mrv +67: JDQ443_atrop3.mrv 67: -67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -95: ..[09:08:15] reactant 2 has no mapped atoms. -95: [09:08:15] reactant 2 has no mapped atoms. -95: [09:08:15] product 1 has no mapped atoms. 67: Test 67: -67: RP-6306_atropBad2.mrv +67: JDQ443_atropBad1.mrv 67: -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -96: [09:08:15] == testCartesianProduct -95: ........[09:08:15] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -95: [09:08:15] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -95: .[09:08:15] reactant atom-mapping number 1 found multiple times. -95: [09:08:15] product atom-mapping number 2 not found in reactants. -95: [09:08:15] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 4 -95: [09:08:15] product atom-mapping number 5 not found in reactants. -103: Finished -103: ----------------------- -103: Test2: Atom Environments -103: Finished -103: ----------------------- -103: Test 3: Atom Environments (Extension) -103: Finished -103: ----------------------- -103: Testing github Issue103: stereochemistry and pathToSubmol -104: Randomness seeded to: 3263048636 -104: --------- -104: =============================================================================== -104: All tests passed (11 assertions in 1 test case) -104: -103: Finished -103: ----------------------- -103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -103: Finished -96: .[09:08:15] == testEnumerateLibrary - 85/230 Test #103: testSubgraphs2 ......................... Passed 0.08 sec - 86/230 Test #104: subgraphsCatch ......................... Passed 0.06 sec -test 105 - Start 105: filterCatalogTest +67: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +87: Randomness seeded to: 3118366735 +87: [17:55:00] Explicit valence for atom # 9 N, 6, is greater than permitted +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +95: ..[17:55:00] reactant 2 has no mapped atoms. +95: [17:55:00] reactant 2 has no mapped atoms. +95: [17:55:00] product 1 has no mapped atoms. + 84/230 Test #91: testReaction ........................... Passed 0.42 sec +test 126 + Start 126: testFingerprints -105: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -105: Test timeout computed to be: 1500 -test 106 - Start 106: pyFilterCatalog +126: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +126: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +126: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [17:55:00] done +114: [17:55:00] ------------------------------------- +114: [17:55:00] PBF edge cases. +114: [17:55:00] done + 85/230 Test #101: pyTautomerQuery ........................ Passed 0.39 sec +test 127 + Start 127: testMHFPFingerprint -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-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -106: Test timeout computed to be: 1500 -96: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -96: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -96: ResourceWarning: Enable tracemalloc to get the object allocation traceback -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: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [09:08:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: Test -67: -67: Sotorasib_atropBad1.mrv -67: -67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +127: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +127: Test timeout computed to be: 1500 +95: ........[17:55:00] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +95: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +95: .[17:55:00] reactant atom-mapping number 1 found multiple times. +95: [17:55:00] product atom-mapping number 2 not found in reactants. +95: [17:55:00] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 4 +95: [17:55:00] product atom-mapping number 5 not found in reactants. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: RP-6306_atrop1.mrv 67: -67: [09:08:15] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -95: ........./build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -95: png = open(fname, 'rb').read() -95: ResourceWarning: Enable tracemalloc to get the object allocation traceback -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 34 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 36 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 38 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 40 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 42 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 87 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 89 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 91 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 93 -95: [09:08:15] Found a SCD/SED line with missing/empty SDT specification at line 95 67: Test 67: -67: Sotorasib_3d.mrv +67: RP-6306_atrop2.mrv 67: 67: Test 67: -67: ZM374979_atrop1.mrv +67: RP-6306_atrop3.mrv 67: 67: Test 67: -67: ZM374979_atrop2.mrv +67: RP-6306_atrop4.mrv 67: 67: Test 67: -67: ZM374979_atrop3.mrv +67: RP-6306_atrop5.mrv 67: +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: Test 67: -67: ZM374979_atropBad1.mrv +67: RP-6306_atropBad1.mrv 67: -67: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -95: ..[09:08:15] SMARTS Parse Error: syntax error while parsing: boromicacid -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -96: ..[09:08:15] == testRGroupState - 87/230 Test #97: pyChemReactionSanitize ................. Passed 0.65 sec -test 107 - Start 107: testFragCatalog - -107: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog -107: Test timeout computed to be: 1500 -95: [09:08:15] reaction has no reactants -95: [09:08:15] reaction has no products -95: [09:08:15] initialization failed -95: [09:08:15] reaction has no reactants -95: [09:08:15] reaction has no products -95: .[09:08:15] SMARTS Parse Error: syntax error while parsing: boromicacid -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -96: .[09:08:15] == testRandomEnumerateAllBBsLibrary +67: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +96: .[17:55:00] == testRandomEnumerateAllBBsLibrary 96: ** [1, 1] 96: ** [0, 2] -96: ** [1, 0] -95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -102: Finished -102: ----------------------- -102: testRootedSubgraphs -102: Finished -102: ----------------------- -102: testRootedPaths -102: Finished -95: [09:08:15] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -95: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -95: [09:08:15] reaction has no reactants -95: [09:08:15] reaction has no products -95: [09:08:15] initialization failed -95: [09:08:15] reaction has no reactants -95: [09:08:15] reaction has no products -95: . -95: ---------------------------------------------------------------------- -95: Ran 54 tests in 0.240s -95: -95: OK - 88/230 Test #102: testSubgraphs1 ......................... Passed 0.34 sec -test 108 - Start 108: pyFragCatalog + 86/230 Test #114: testPBF ................................ Passed 0.28 sec +test 128 + Start 128: testFingerprintGenerators -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-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -108: Test timeout computed to be: 1500 -95: ******************************************** -95: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -95: -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: [09:08:15] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -96: .[09:08:15] == testRandomEnumerateLibrary -107: 21 -68: [09:08:15] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [09:08:15] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -96: .[09:08:15] == testRandomSample -96: .[09:08:15] == testRandomSampleAllBBs -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: [09:08:15] initialization failed -96: .[09:08:15] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -96: [09:08:15] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -96: .[09:08:15] == testRemoveBadMatches -96: .[09:08:15] == testTimings -105: Warning: molecule failed filter -105: Warning: molecule failed filter: reason hzone_phenol_A(479) -105: v = { -105: 0,23}, -105: 1,22}, -105: 2,20}, -105: 3,19}, -105: 4,25}, -105: 5,24}, -105: 6,18}, -105: 7,17}, -105: 8,16}, -105: 9,21}, -105: } -105: match = { -105: 0,23}, -105: 1,22}, -105: 2,20}, -105: 3,19}, -105: 4,25}, -105: 5,24}, -105: 6,18}, -105: 7,17}, -105: 8,16}, -105: 9,21}, -105: } -105: Warning: molecule failed filter -105: Warning: molecule failed filter: reason cyano_imine_B(17) -105: v = { -105: 0,11}, -105: 1,12}, -105: 2,13}, -105: 3,14}, -105: 4,15}, -105: 5,10}, -105: 6,9}, -105: 7,8}, -105: 8,7}, -105: 9,6}, -105: 10,5}, -105: 11,17}, -105: 12,16}, -105: } -105: match = { -105: 0,11}, -105: 1,12}, -105: 2,13}, -105: 3,14}, -105: 4,15}, -105: 5,10}, -105: 6,9}, -105: 7,8}, -105: 8,7}, -105: 9,6}, -105: 10,5}, -105: 11,17}, -105: 12,16}, -105: } -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: } -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: Test -67: -67: NewChiralTest -67: -67: Test -67: -67: NewChiralTestNoChiral -67: -67: Test -67: -67: NewChiralTestNoChiral -67: -67: Test -67: -67: NewChiralTest2 -67: -67: Test -67: -67: NewChiralTest2 -67: -67: Test -67: -67: NewChiralTest2AllChiral -67: -67: Test -67: -67: NewChiralTest2AllChiral -67: -67: Test -67: -67: Vendor839 -67: -67: Test -67: -67: DoubleBondChain -67: -67: Test -67: -67: Na_Mg_Al_OH -67: -67: Test -67: -67: Pb -67: -67: Test -67: -67: O_Mg_Si -67: -67: Test -67: -67: SquiggleBond -67: -67: Test -67: -67: BigMacrocycle -67: +128: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 200 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: -67: Smiles1 +67: RP-6306_atropBad2.mrv 67: - 89/230 Test #67: testMrvToMol ........................... Passed 2.13 sec -test 109 - Start 109: testDescriptors - -109: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -109: Test timeout computed to be: 1500 - 90/230 Test #95: pyChemReactions ........................ Passed 0.90 sec -test 110 - Start 110: testAUTOCORR2D - -110: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -110: Test timeout computed to be: 1500 -101: ..... -101: ---------------------------------------------------------------------- -101: Ran 5 tests in 0.043s -101: -101: OK -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Crippen parameter acquisition. -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Crippen calculation. -68: [09:08:15] Empty atom list: 'M ALS 1 0 F' on line 8. -68: de_DE.UTF-8 -68: [09:08:15] ------------------------------------- -68: [09:08:15] Test multithreading Locale Switching -110: [09:08:15] ---------------------------- -110: start test autocorr2D -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Issue262: problems with Crippen calculation from pickles. -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test AMW calculation. -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Exact MW calculation. -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Labute ASA descriptors. -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test TPSA descriptors. - 91/230 Test #101: pyTautomerQuery ........................ Passed 0.62 sec -test 111 - Start 111: testATF - -111: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF -111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 -109: [09:08:15] done -109: [09:08:15] ------------------------------------- -109: [09:08:15] Test Lipinski parameters. - 92/230 Test #111: testATF ................................ Passed 0.04 sec -test 112 - Start 112: testBCUT - -112: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -112: Test timeout computed to be: 1500 -112: [09:08:15] ------------------------------------- -112: [09:08:15] Basic BCUT tests. -68: [09:08:15] Test multithreading (Done) -68: [09:08:15] ------------------------------------- -112: [09:08:15] done -112: [09:08:15] ------------------------------------- -112: [09:08:15] Larger BCUT tests. -68: *************************************** -68: *************************************** -68: [09:08:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [09:08:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [09:08:16] bond with order 0 found on line 7. This is not part of the MDL specification. -109: [09:08:16] done -109: [09:08:16] ------------------------------------- -109: [09:08:16] Test VSA descriptors. -109: [09:08:16] done -109: [09:08:16] ------------------------------------- -109: [09:08:16] Test molecular formula calculation. -109: [09:08:16] done -109: [09:08:16] ------------------------------------- -109: [09:08:16] Test Issue 3415534. -109: [09:08:16] done -109: [09:08:16] ------------------------------------- -109: [09:08:16] Test Issue3433771: Bad definition for Crippen atom type O11. -109: [09:08:16] done -109: [09:08:16] ------------------------------------- -109: [09:08:16] Test multithreading -109: reading molecules -68: [09:08:16] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [09:08:16] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [09:08:16] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. - 93/230 Test #105: filterCatalogTest ...................... Passed 0.52 sec -test 113 - Start 113: testEEM - -113: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM -113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -109: processing -109: launch :0 -109: launch :1 -109: launch :2 -109: launch :3 -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 -113: =>start test EEM -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 0 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110: [09:08:16] done -110: [09:08:16] ------------------------------------- -110: [09:08:16] Test Github #3806: NaNs from AUTOCORR2D descriptor -110: [09:08:16] done -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 94/230 Test #110: testAUTOCORR2D ......................... Passed 0.66 sec -test 114 - Start 114: testPBF - -114: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF -114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 100 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: ......... -108: ---------------------------------------------------------------------- -108: Ran 9 tests in 0.107s -108: -108: OK -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [09:08:16] ------------------------------------- -114: [09:08:16] Basic PBF tests. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [09:08:16] ------------------------------------- -112: [09:08:16] Test empty molecule BCUT. - 95/230 Test #112: testBCUT ............................... Passed 0.63 sec -test 115 - Start 115: testRDFcustom - -115: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 96/230 Test #108: pyFragCatalog .......................... Passed 1.02 sec -test 116 - Start 116: testRDF - -116: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -39: [09:08:16] done: 500000 -39: [09:08:16] Done -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 200 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -39: [09:08:16] Testing hanoi with a functor. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -39: [09:08:16] Done -39: [09:08:16] Testing basic partition refinement. -39: [09:08:16] Done -39: [09:08:16] Testing partition refinement with neighbors. -39: [09:08:16] Done -39: [09:08:16] testing canonicalization via tie breaking. -39: [09:08:16] Done -39: [09:08:16] testing canonicalization using the wrapper. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -39: [09:08:16] Done -39: [09:08:16] testing some specific ordering problems -39: [09:08:16] Finished -39: [09:08:16] testing chiral invariants. -39: [09:08:16] Finished -39: [09:08:16] testing unique ranks in w.r.t. renumbering. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -39: [09:08:16] Finished -39: [09:08:16] testing mol fragments. -39: [09:08:16] Finished -39: [09:08:16] testing protein round-tripping. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: Randomness seeded to: 2322531019 -87: [09:08:16] Explicit valence for atom # 9 N, 6, is greater than permitted -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 300 -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [09:08:17] done -114: [09:08:17] ------------------------------------- -114: [09:08:17] PBF edge cases. -114: [09:08:17] done -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 97/230 Test #114: testPBF ................................ Passed 0.69 sec -test 117 - Start 117: testMORSE - -117: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 400 -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -107: [09:08:17] -107: -107: **** -107: Invariant Violation -107: nonsense -107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -107: Failed Expression: token != tokens.end() -107: ---------- -107: Stacktrace: -107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 -107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: ---------- -107: **** -107: -107: [09:08:17] -107: -107: **** -107: Invariant Violation -107: nonsense no new line -107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -107: Failed Expression: token != tokens.end() -107: ---------- -107: Stacktrace: -107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 -107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: ---------- -107: **** -107: -107: [09:08:17] -107: -107: **** -107: Invariant Violation -107: nonsense with tab -107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -107: Failed Expression: token != tokens.end() -107: ---------- -107: Stacktrace: -107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x00007F2F2883EEFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x000055B3F0B2B183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x000055B3F0B28731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x00007F2F27A31D68 in /lib/x86_64-linux-gnu/libc.so.6 -107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -107: 8# 0x000055B3F0B28861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: ---------- -107: **** -107: -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 98/230 Test #107: testFragCatalog ........................ Passed 1.60 sec -test 118 - Start 118: test3D - -118: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D -118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: [09:08:17] ------------------------------------- -118: [09:08:17] Basic PMI tests. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [09:08:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: Elapsed time: 1.21878 s -113: Errors:0 -113: [09:08:17] test on : 500 molecules done - 99/230 Test #113: testEEM ................................ Passed 1.27 sec -test 119 - Start 119: testWHIM - -119: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM -119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:17] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [09:08:17] 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: [09:08:17] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0x00007FE02B6C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0x00007FE02B6D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# 0x00007FE02B6D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 6# 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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 9# 0x0000556B52AD1CF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x0000556B52B384F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0x0000556B52AB89E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 12# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 14# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] More PMI/NPR tests. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] Basic NPR tests. -106: .............[09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -106: [09:08:17] SMILES Parse Error: syntax error while parsing: --- -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [09:08:17] dasfsadf -87: [09:08:17] Explicit valence for atom # 3 Al, 6, is greater than permitted -39: [09:08:17] Finished -39: [09:08:17] testing stability w.r.t. renumbering. -106: .[09:08:17] SMILES Parse Error: syntax error while parsing: mydoghasfleas -106: [09:08:17] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -39: [09:08:17] Finished -39: [09:08:17] testing smiles round-tripping. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] PMI edge cases. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] NPR edge cases. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] 3D descriptors. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] 3D descriptor edge cases. -118: [09:08:17] done -118: [09:08:17] ------------------------------------- -118: [09:08:17] Inertial shape factor. -118: [09:08:17] done -100/230 Test #118: test3D ................................. Passed 0.59 sec -test 120 - Start 120: testGETAWAY - -120: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -120: Test timeout computed to be: 1500 -68: [09:08:17] 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: [09:08:17] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -87: [09:08:17] Explicit valence for atom # 4 Al, 6, is greater than permitted -96: . -96: ---------------------------------------------------------------------- -96: Ran 11 tests in 2.387s -96: -96: OK -96: True -96: == CartesianProductStrategy CartesianProductStrategy -96: 197 out of 300 -96: 0 6 out of 10 -96: 1 3 out of 5 -96: 2 4 out of 6 -96: 198 out of 300 -96: 0 10 out of 10 -96: 1 5 out of 5 -96: 2 6 out of 6 -96: Skipped 10000000 in 0.14346098899841309 seconds -96: Skipped 10000000 in 1.4000003337860107 seconds -96: Skipped 10000000 in 0.31561708450317383 seconds -39: [09:08:17] Finished -39: [09:08:17] testing github #1567: Non-canonical result from MolFragmentToSmiles() -39: [09:08:17] Finished -101/230 Test #39: hanoiTest .............................. Passed 4.91 sec -test 121 - Start 121: testAUTOCORR3D - -121: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -121: Test timeout computed to be: 1500 -87: [09:08:18] Explicit valence for atom # 10 Si, 6, is greater than permitted -68: ---------------------------------- -68: ---------------------------------- -68: [09:08:18] -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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x0000556B52ADF0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x0000556B52B3856A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x0000556B52AB89E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0x00007FE02AC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 8# 0x0000556B52AB8B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: -68: [09:08:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -106: ....... -106: ---------------------------------------------------------------------- -106: Ran 21 tests in 2.022s -106: -106: OK -106: (Five aromatic carbons And (Not any of Five aromatic carbons)) -106: (Five aromatic carbons Or (Not any of Five aromatic carbons)) -106: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) -106: ******************************************** -106: Testing: PAINS_A 2 -106: ******************************************** -106: Testing: PAINS_B 4 -106: ******************************************** -106: Testing: PAINS_C 8 -106: ******************************************** -106: Testing: PAINS 14 -106: (Not FilterMatcher) -106: Bar -106: Count 1 -106: ******************************************** -106: {'Cl,Br,I'} -106: 1 -106: 2 -106: running -102/230 Test #96: pyChemReactionEnumerations ............. Passed 3.15 sec -test 122 - Start 122: testCoulombMat - -122: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -122: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -122: Test timeout computed to be: 1500 -122: ===================== Testing CoulombMat ======================= -122: CM test 1 mat Done -103/230 Test #122: testCoulombMat ......................... Passed 0.05 sec -test 123 - Start 123: descriptorsTestCatch - -123: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -123: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -123: Test timeout computed to be: 1500 -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -123: Randomness seeded to: 3502967058 +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +96: ** [1, 0] +123: Randomness seeded to: 3083320467 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 + 87/230 Test #97: pyChemReactionSanitize ................. Passed 0.42 sec +test 129 + Start 129: fpTestCatch + +129: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +129: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +129: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +96: .[17:55:00] == testRandomEnumerateLibrary 123: Warning: Atom Count for residue ARG64A does not match expected count 123: Warning: Atom Count for residue LYS80A does not match expected count -104/230 Test #106: pyFilterCatalog ........................ Passed 2.71 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -124: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 123: Warning: Atom Count for residue GLU150A does not match expected count 123: Warning: Atom Count for residue ASN157A does not match expected count -119: =>start test WHIM -119: [09:08:18] test on : 365 molecules done -105/230 Test #119: testWHIM ............................... Passed 0.95 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -125: Test timeout computed to be: 1500 -27: All 191 tests passed -123: Warning: Atom Count for residue GLU5A does not match expected count -116: =>start test rdf -116: [09:08:18] test on : 365 molecules done -106/230 Test #116: testRDF ................................ Passed 1.84 sec -test 126 - Start 126: testFingerprints - -126: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -126: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -126: 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... +127: [17:55:00] ------------------------------------- +127: [17:55:00] Test MHFP fingerprint encoder initialization +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: 126: 126: @@ -25603,6 +24397,7 @@ 126: 0 0->1 order: 1 conj?: 1 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: 3 3->4 order: a conj?: 1 aromatic?: 1 126: 4 4->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 @@ -25659,6 +24454,8 @@ 126: 126: ------------------- 126: +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test atom-pair fp generator 126: SMI: c1(O)cc2[nH]cnc2c(O)n1 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 @@ -25696,6 +24493,8 @@ 126: 126: ------------------- 126: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +96: .[17:55:00] == testRandomSample 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 @@ -25733,6 +24532,7 @@ 126: 126: ------------------- 126: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: SMI: c12cc(O)nc(O)c1nc[nH]2 126: Atoms: 126: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 @@ -25788,6 +24588,7 @@ 126: 1 1->2 order: a conj?: 1 aromatic?: 1 126: 2 2->3 order: a conj?: 1 aromatic?: 1 126: 3 3->4 order: 1 conj?: 1 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: 4 3->5 order: a conj?: 1 aromatic?: 1 126: 5 5->6 order: a conj?: 1 aromatic?: 1 126: 6 6->7 order: 1 conj?: 1 @@ -25963,6 +24764,37 @@ 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 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +96: .[17:55:00] == testRandomSampleAllBBs 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 @@ -26050,716 +24882,700 @@ 126: 126: ------------------- 126: -68: [09:08:18] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [09:08:18] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Morgan Fingerprints. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Morgan Fingerprints using fromAtoms argument. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Morgan Fingerprints as bit vects. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Morgan Fingerprints with feature invariants. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test additional Morgan fingerprints options. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Atom Codes. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Atom Pairs. -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Atom Pairs part 2. -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Topological Torsions. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Bulk Topological Torsions. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: =>start test rdf custom -115: [09:08:18] test on : 365 molecules done -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -121: =>start test autocorr3D -121: [09:08:18] test on : 365 molecules done -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -107/230 Test #121: testAUTOCORR3D ......................... Passed 0.78 sec -test 127 - Start 127: testMHFPFingerprint - -127: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -127: Test timeout computed to be: 1500 -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: [09:08:18] ------------------------------------- -127: [09:08:18] Test MHFP fingerprint encoder initialization -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -68: [09:08:18] Empty atom list: 'M ALS 1 0 F' on line 8. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -108/230 Test #68: fileParsersTest1 ....................... Passed 5.19 sec -test 128 - Start 128: testFingerprintGenerators - -128: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: [09:08:18] done -127: [09:08:18] ------------------------------------- -127: [09:08:18] Test MHFP shingling creation -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ..[09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: .[09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: ..[09:08:18] -124: -124: **** -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: Pre-condition Violation -124: Number of atom props not equal to number of atoms -124: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp -124: Failed Expression: atom_props.size() == num_atoms -124: ---------- -124: Stacktrace: -124: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -124: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -124: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 -124: 3# 0x00007F90CECA25D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -124: 4# 0x00007F90CECB2256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -124: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -124: 6# 0x00007F90D330B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -124: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -124: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -124: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -124: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -124: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -124: 12# 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-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -124: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -124: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -124: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -124: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 17# 0x00007F90D09AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 18# 0x00007F90D09AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 19# 0x00007F90D09AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 20# 0x00007F90D09AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 21# 0x00007F90D09AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -124: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so -124: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so -124: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so -124: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so -124: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -124: 27# 0x00007F90D33083C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -124: 28# _PyObject_MakeTpCall in /usr/bin/python3 -124: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 30# 0x0000000000546E76 in /usr/bin/python3 -124: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 32# _PyObject_Call_Prepend in /usr/bin/python3 -124: 33# 0x000000000059D6E4 in /usr/bin/python3 -124: 34# _PyObject_MakeTpCall in /usr/bin/python3 -124: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 36# 0x0000000000546E76 in /usr/bin/python3 -124: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 38# _PyObject_Call_Prepend in /usr/bin/python3 -124: 39# 0x000000000059D6E4 in /usr/bin/python3 -124: 40# _PyObject_MakeTpCall in /usr/bin/python3 -124: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 42# 0x0000000000546E76 in /usr/bin/python3 -124: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 44# _PyObject_Call_Prepend in /usr/bin/python3 -124: 45# 0x000000000059D6E4 in /usr/bin/python3 -124: 46# _PyObject_MakeTpCall in /usr/bin/python3 -124: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 48# _PyObject_Call_Prepend in /usr/bin/python3 -124: 49# 0x000000000059810D in /usr/bin/python3 -124: 50# 0x0000000000593E22 in /usr/bin/python3 -124: 51# _PyObject_MakeTpCall in /usr/bin/python3 -124: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 53# PyEval_EvalCode in /usr/bin/python3 -124: 54# 0x00000000005FFE7F in /usr/bin/python3 -124: 55# 0x00000000006A59F2 in /usr/bin/python3 -124: 56# _PyRun_SimpleFileObject in /usr/bin/python3 -124: 57# _PyRun_AnyFileObject in /usr/bin/python3 -124: 58# Py_RunMain in /usr/bin/python3 -124: 59# Py_BytesMain in /usr/bin/python3 -124: 60# 0x00007F90D3AE1D68 in /lib/x86_64-linux-gnu/libc.so.6 -124: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -124: 62# _start in /usr/bin/python3 -124: ---------- -124: **** -124: -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test atom-pair fp generator -127: [09:08:18] done -127: [09:08:18] ------------------------------------- -127: [09:08:18] Test MHFP hashing of string and uint arrays -127: [09:08:18] done -127: [09:08:18] ------------------------------------- -127: [09:08:18] Test SECFP fingerprint functionality -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test atom-pair fp generator with different arguments -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -124: ...Warning: Atom Count for residue GLU5A does not match expected count -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -127: [09:08:18] done -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: Warning: Atom Count for residue ASN39A does not match expected count -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test atom-pair additional output -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Folded Atom Pairs. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Rooted Atom Pairs. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test ignoring atoms in Atom Pairs. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Atom Pairs including info about chirality. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Morgan Fingerprints. -124: Warning: Atom Count for residue GLU53A does not match expected count -109/230 Test #127: testMHFPFingerprint .................... Passed 0.15 sec -test 129 - Start 129: fpTestCatch - -129: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -129: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -129: Test timeout computed to be: 1500 -124: Warning: Atom Count for residue ARG64A does not match expected count -124: Warning: Atom Count for residue LYS80A does not match expected count -124: Warning: Atom Count for residue GLU150A does not match expected count -124: Warning: Atom Count for residue ASN157A does not match expected count -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test morgan fp generator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Morgan Fingerprints using fromAtoms argument. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Morgan Fingerprints as bit vects. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test Morgan Fingerprints with feature invariants. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test additional Morgan fingerprints options. -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Single atoms setting radius 1 bits in Morgan fingerprints -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test different invariant generator combinations -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test invariant overriding -128: [09:08:18] done -128: [09:08:18] ------------------------------------- -128: [09:08:18] Test RDKit fp generator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -87: [09:08:18] Explicit valence for atom # 2 O, 4, is greater than permitted -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Hashed Atom Pairs. -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Hashed torsions. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Rooted Atom Pairs. -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test ignoring atoms in Atom Pairs. -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test Rooted Topological Torsions. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test ignoring atoms in Topological Torsions. -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test atom info from morgan fingerprints. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] Test atom info from morgan fingerprints including Info Redundant Environments. -126: [09:08:18] done -126: [09:08:18] ------------------------------------- -126: [09:08:18] ------------------------------------- -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:18] ------------------------------------- -129: Randomness seeded to: 3789818418 -129: =============================================================================== -129: All tests passed (188 assertions in 16 test cases) -129: -110/230 Test #129: fpTestCatch ............................ Passed 0.09 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test atom-pair fp generator with different arguments +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +96: .[17:55:00] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +96: [17:55:00] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +96: .[17:55:00] == testRemoveBadMatches +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +113: [17:55:00] 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: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +108: ......... +108: ---------------------------------------------------------------------- +108: Ran 9 tests in 0.068s +108: +108: OK +96: .[17:55:00] == testTimings +95: ........./build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +95: png = open(fname, 'rb').read() +95: ResourceWarning: Enable tracemalloc to get the object allocation traceback +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 34 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 36 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 38 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 40 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 42 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 87 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 89 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 91 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 93 +95: [17:55:00] Found a SCD/SED line with missing/empty SDT specification at line 95 +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Morgan Fingerprints. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] done +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Morgan Fingerprints using fromAtoms argument. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Morgan Fingerprints as bit vects. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Morgan Fingerprints with feature invariants. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test additional Morgan fingerprints options. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Atom Codes. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Atom Pairs. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Atom Pairs part 2. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Topological Torsions. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Bulk Topological Torsions. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +110: [17:55:00] done +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +110: [17:55:00] ------------------------------------- +110: [17:55:00] Test Github #3806: NaNs from AUTOCORR2D descriptor +110: [17:55:00] done +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 88/230 Test #110: testAUTOCORR2D ......................... Passed 0.37 sec test 130 Start 130: fpGenTestCatch 130: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 130: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 -126: [09:08:19] ------------------------------------- -126: [09:08:19] ------------------------------------- -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test Atom Pairs including info about chirality. -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test Topological Torsions including info about chirality. -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test GitHub Issue 25: fingerprint backwards compatibility. -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test GitHub Issue 151: PatternFingerprint problems -87: [09:08:19] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [09:08:19] Explicit valence for atom # 3 Be, 4, is greater than permitted -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test 3D atom pairs. -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -126: [09:08:19] done -126: [09:08:19] ------------------------------------- -126: [09:08:19] Test multithreading with the pattern FP -126: reading molecules -124: Warning: Atom Count for residue GLU5A does not match expected count -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 5.973s -12: -12: OK -126: pass 1 -126: launch :0 -126: launch :1 -126: launch :2 -126: launch :3 -111/230 Test #41: resMolSupplierTest ..................... Passed 6.04 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +66: ..............[17:55:00] SMILES Parse Error: syntax error while parsing: invalidsmiles +66: [17:55:00] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +95: ..[17:55:00] SMARTS Parse Error: syntax error while parsing: boromicacid +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +95: [17:55:00] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +95: [17:55:00] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +95: [17:55:00] reaction has no reactants +95: [17:55:00] reaction has no products +95: [17:55:00] initialization failed +95: [17:55:00] reaction has no reactants +95: [17:55:00] reaction has no products +128: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test atom-pair additional output +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Folded Atom Pairs. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Rooted Atom Pairs. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test ignoring atoms in Atom Pairs. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Atom Pairs including info about chirality. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Morgan Fingerprints. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test morgan fp generator +127: [17:55:00] done +127: [17:55:00] ------------------------------------- +127: [17:55:00] Test MHFP shingling creation +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +129: Randomness seeded to: 2281545529 +129: =============================================================================== +129: All tests passed (188 assertions in 16 test cases) +129: +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 89/230 Test #129: fpTestCatch ............................ Passed 0.06 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-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 131: Test timeout computed to be: 1500 -87: [09:08:19] Explicit valence for atom # 27 P, 6, is greater than permitted -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test unfolded version of RDKFP -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test topological torsion fp generator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -112/230 Test #12: pyBV ................................... Passed 6.53 sec +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +95: .[17:55:00] SMARTS Parse Error: syntax error while parsing: boromicacid +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +95: [17:55:00] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +95: [17:55:00] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +95: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +95: [17:55:00] reaction has no reactants +95: [17:55:00] reaction has no products +95: [17:55:00] initialization failed +95: [17:55:00] reaction has no reactants +95: [17:55:00] reaction has no products +95: . +95: ---------------------------------------------------------------------- +95: Ran 54 tests in 0.154s +95: +95: OK +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Morgan Fingerprints using fromAtoms argument. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Morgan Fingerprints as bit vects. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Morgan Fingerprints with feature invariants. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test additional Morgan fingerprints options. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Single atoms setting radius 1 bits in Morgan fingerprints +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test different invariant generator combinations +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test invariant overriding +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test RDKit fp generator +95: ******************************************** +95: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +95: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +127: [17:55:00] done +127: [17:55:00] ------------------------------------- +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +127: [17:55:00] Test MHFP hashing of string and uint arrays +127: [17:55:00] done +127: [17:55:00] ------------------------------------- +127: [17:55:00] Test SECFP fingerprint functionality +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] More PMI/NPR tests. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +118: [17:55:00] Basic NPR tests. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +90: Randomness seeded to: 2762720323 +90: =============================================================================== +90: All tests passed (11480 assertions in 38 test cases) +90: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 90/230 Test #90: testGenericGroups ...................... Passed 0.55 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-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 132: Test timeout computed to be: 1500 -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test Topological Torsions. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test Folded torsions. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test Bulk Topological Torsions. -130: Randomness seeded to: 1044882225 -130: =============================================================================== -130: All tests passed (2692 assertions in 5 test cases) -130: -113/230 Test #130: fpGenTestCatch ......................... Passed 0.41 sec +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +127: [17:55:00] done +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 91/230 Test #108: pyFragCatalog .......................... Passed 0.46 sec + 92/230 Test #127: testMHFPFingerprint .................... Passed 0.12 sec test 133 Start 133: testPartialCharges 133: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 133: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 133: Test timeout computed to be: 1500 -123: Warning: Atom Count for residue ASN39A does not match expected count -117: =>start test MORSE -117: =>read file -117: [09:08:19] test on : 365 molecules done -114/230 Test #133: testPartialCharges ..................... Passed 0.07 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-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 134: Test timeout computed to be: 1500 -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test Rooted Topological Torsions. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test ignoring atoms in Topological Torsions. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test Topological Torsions including info about chirality. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test convenience and bulk fp calculation functions -115/230 Test #117: testMORSE .............................. Passed 2.38 sec +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +123: Warning: Atom Count for residue GLU5A does not match expected count +28: ... +28: ---------------------------------------------------------------------- +28: Ran 12 tests in 0.557s +28: +28: OK +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +87: [17:55:00] Explicit valence for atom # 3 Al, 6, is greater than permitted +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: 300 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 93/230 Test #95: pyChemReactions ........................ Passed 0.57 sec test 135 Start 135: testMolTransforms 135: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 135: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 135: Test timeout computed to be: 1500 -126: pass 2 -126: launch :0 -126: launch :1 -126: launch :2 -126: launch :3 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 94/230 Test #133: testPartialCharges ..................... Passed 0.05 sec +test 136 + Start 136: molTransformsTestCatch + +136: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +136: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +67: Test +67: +67: BMS-986142_atropBad2.mrv +67: +67: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: Randomness seeded to: 2119916496 +130: =============================================================================== +130: All tests passed (2692 assertions in 5 test cases) +130: +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 95/230 Test #130: fpGenTestCatch ......................... Passed 0.12 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-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +137: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +87: [17:55:00] Explicit valence for atom # 4 Al, 6, is greater than permitted +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator 135: *********************************************************** 135: Testing MolTransforms 135: --------------------------------- @@ -26790,96 +25606,462 @@ 135: testWeightedCentroid 135: 135: *********************************************************** -116/230 Test #135: testMolTransforms ...................... Passed 0.08 sec -test 136 - Start 136: molTransformsTestCatch - -136: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -136: Test timeout computed to be: 1500 -136: Randomness seeded to: 698560435 -136: =============================================================================== -136: All tests passed (4 assertions in 1 test case) -136: -117/230 Test #136: molTransformsTestCatch ................. Passed 0.08 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-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -137: Test timeout computed to be: 1500 -125: ........ -125: ---------------------------------------------------------------------- -125: Ran 8 tests in 0.490s -125: -125: OK -123: Warning: Atom Count for residue GLU53A does not match expected count -131: .............. -131: ---------------------------------------------------------------------- -131: Ran 14 tests in 0.259s -131: -131: OK -128: [09:08:19] done -128: [09:08:19] ------------------------------------- -128: [09:08:19] Test GitHub Issue #6958 -128: [09:08:19] DEPRECATION WARNING: please use AtomPairGenerator -118/230 Test #128: testFingerprintGenerators .............. Passed 1.14 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] 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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 + 96/230 Test #135: testMolTransforms ...................... Passed 0.05 sec test 138 Start 138: forceFieldHelpersCatch 138: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 138: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers 138: Test timeout computed to be: 1500 -123: Warning: Atom Count for residue ARG64A does not match expected count -138: Randomness seeded to: 2573869229 -138: =============================================================================== -138: All tests passed (11 assertions in 1 test case) -138: -119/230 Test #138: forceFieldHelpersCatch ................. Passed 0.06 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Hashed Atom Pairs. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Hashed torsions. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Rooted Atom Pairs. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test ignoring atoms in Atom Pairs. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Rooted Topological Torsions. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test ignoring atoms in Topological Torsions. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test atom info from morgan fingerprints. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test atom info from morgan fingerprints including Info Redundant Environments. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +136: Randomness seeded to: 3777695282 +136: =============================================================================== +136: All tests passed (4 assertions in 1 test case) +136: + 97/230 Test #28: pyForceFieldConstraints ................ Passed 0.87 sec + 98/230 Test #136: molTransformsTestCatch ................. Passed 0.05 sec test 139 Start 139: testMMFFForceFieldHelpers 139: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 139: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 139: Test timeout computed to be: 1500 -120/230 Test #131: pyTestGenerator ........................ Passed 0.91 sec test 140 Start 140: testMMFFForceFieldHelpersMultiThread 140: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 140: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 140: Test timeout computed to be: 1500 -139: [09:08:20] ------------------------------------- -139: [09:08:20] Test MMFF atom types. -115: =>start test morse custom -115: [09:08:20] test on : 365 molecules done -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing MMFF builder tools. -140: [09:08:20] ------------------------------------- -140: [09:08:20] Test MMFF multithreading -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing MMFF builder+minimization. -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing Issue239. -134: ....... -134: ---------------------------------------------------------------------- -134: Ran 7 tests in 0.163s -134: -134: OK -124: Warning: Atom Count for residue ASN39A does not match expected count -121/230 Test #125: pyMolDescriptors3D ..................... Passed 1.95 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] ------------------------------------- +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] ------------------------------------- +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: Test +67: +67: RP-6306_atropBad1.mrv +67: +67: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +3: dynamic RDAny:0.390304 s +3: static RDValue:1e-06 s +66: ..... +66: ---------------------------------------------------------------------- +66: Ran 19 tests in 0.449s +66: +66: OK +113: [17:55:00] 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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] ------------------------------------- +126: [17:55:00] ------------------------------------- +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Atom Pairs including info about chirality. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test Topological Torsions including info about chirality. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test GitHub Issue 25: fingerprint backwards compatibility. +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test GitHub Issue 151: PatternFingerprint problems +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test 3D atom pairs. +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:00] DEPRECATION WARNING: please use AtomPairGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +126: [17:55:00] done +126: [17:55:00] ------------------------------------- +126: [17:55:00] Test multithreading with the pattern FP +126: reading molecules +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +140: [17:55:00] ------------------------------------- +140: [17:55:00] Test MMFF multithreading +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +138: Randomness seeded to: 4105993836 +138: =============================================================================== +138: All tests passed (11 assertions in 1 test case) +138: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 99/230 Test #138: forceFieldHelpersCatch ................. Passed 0.04 sec test 141 Start 141: testUFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 141: Test timeout computed to be: 1500 -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing calcEnergy with passed coords. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: [17:55:00] Explicit valence for atom # 10 Si, 6, is greater than permitted +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: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: Sotorasib_atropBad1.mrv +67: +67: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +139: [17:55:00] ------------------------------------- +139: [17:55:00] Test MMFF atom types. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: [17:55:00] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +119: =>start test WHIM +119: [17:55:00] test on : 365 molecules done +115: =>start test rdf custom +115: [17:55:00] test on : 365 molecules done +100/230 Test #119: testWHIM ............................... Passed 0.44 sec +test 142 + Start 142: testCrystalForceField + +142: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +142: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +142: Test timeout computed to be: 1500 +113: 400 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing MMFF builder tools. +126: pass 1 +126: launch :0 +126: launch :1 +126: launch :2 +126: launch :3 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +3: dynamic RDValue:0.064249 s +3: deleted! +3: [17:55:00] ------------------------------------- +3: [17:55:00] Testing String Pickle Roundtrips. +3: [17:55:00] done +3: [17:55:00] ------------------------------------- +3: [17:55:00] Testing conversion of vect to string. +3: [17:55:00] done +3: [17:55:00] ------------------------------------- +3: [17:55:00] Testing returning const references. +3: [17:55:00] any cast +3: [17:55:00] done: 0.0013 300000 +3: [17:55:00] copy +3: [17:55:00] done: 0.00135 300000 +3: [17:55:00] ref +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +3: [17:55:00] done: 0.001262 300000 +3: [17:55:00] dict +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101/230 Test #66: pyDepictor ............................. Passed 0.83 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-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap +143: Test timeout computed to be: 1500 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +3: [17:55:00] done: 0.002931 300000 +3: [17:55:00] ref with hasVal +141: [17:55:00] ------------------------------------- +141: [17:55:00] Test UFF atom labels. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +3: [17:55:00] done: 0.002019 300000 +3: [17:55:00] done +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +3: [17:55:00] ------------------------------------- +3: [17:55:00] Testing dict update. +3: [17:55:00] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102/230 Test #3: testDict ............................... Passed 1.00 sec +test 144 + Start 144: testDistGeomHelpers + +144: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers +144: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +144: Test timeout computed to be: 1500 +142: ------------------------------------- +142: Test CrystalFF torsional term. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 140: processing 140: launch :0 140: launch :1 @@ -26901,896 +26083,551 @@ 140: launch :17 140: launch :18 140: launch :19 +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing MMFF builder+minimization. 140: launch :20 140: launch :21 140: launch :22 140: launch :23 -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing calcGrad. -141: [09:08:20] ------------------------------------- -141: [09:08:20] Test UFF atom labels. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Test UFF atom typer. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing UFF builder tools. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing UFF builder+minimization. -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing Issue242. -122/230 Test #134: pyPartialCharges ....................... Passed 0.89 sec -test 142 - Start 142: testCrystalForceField - -142: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -142: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -142: Test timeout computed to be: 1500 -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing github 308: crash during MMFF parameterization . -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing SFIssue1653802. -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Testing SFIssue2378119. -139: [09:08:20] done -139: [09:08:20] ------------------------------------- -139: [09:08:20] Test MMFF force-field parameter getters. -139: [09:08:20] ------------------------------------- -139: [09:08:20] Test MMFF multithreading -139: generating reference data -142: ------------------------------------- -142: Test CrystalFF torsional term. -115: =>start test AUTOCORR3D custom -115: [09:08:20] test on : 365 molecules done -123: Warning: Atom Count for residue LYS80A does not match expected count -132: .. -132: ---------------------------------------------------------------------- -132: Ran 2 tests in 0.070s -132: -132: OK -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing UFF special cases. -141: [09:08:20] UFFTYPER: Unrecognized charge state for atom: 0 -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing Issue239. -124: Warning: Atom Count for residue GLU53A does not match expected count -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing calcEnergy with passed coords. -123/230 Test #132: pyTestMHFP ............................. Passed 1.39 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-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap -143: Test timeout computed to be: 1500 -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing calcGrad. -115: =>start test 2 WHIM custom -115: [09:08:20] test on : 365 molecules done -124/230 Test #142: testCrystalForceField .................. Passed 0.41 sec -test 144 - Start 144: testDistGeomHelpers - -144: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers -144: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -144: Test timeout computed to be: 1500 -137: ........ -137: ---------------------------------------------------------------------- -137: Ran 8 tests in 0.095s -137: -137: OK -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing SFIssue1653802. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing SFIssue2378119. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Test UFF force-field parameter getters. -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing handling missing parameters. -141: [09:08:20] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [09:08:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -141: [09:08:20] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [09:08:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -144: [09:08:20] ******************************************************** -144: [09:08:20] Testing DistGeomHelpers -144: [09:08:20] --------------------------------- -144: [09:08:20] test2 -144: -144: go -144: ------------------------------------- -144: -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Testing SFIssue3009337. -141: [09:08:20] done -141: [09:08:20] ------------------------------------- -141: [09:08:20] Test UFF multithreading -140: done -140: [09:08:20] done -141: generating reference data -124: Warning: Atom Count for residue ARG64A does not match expected count -115: =>start test 1 WHIM custom -115: [09:08:21] test on : 365 molecules done -125/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.97 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Test UFF atom typer. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] 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: [17:55:00] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing UFF builder tools. +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing UFF builder+minimization. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [17:55:00] ------------------------------------- +112: [17:55:00] Test empty molecule BCUT. +103/230 Test #112: testBCUT ............................... Passed 0.62 sec test 145 Start 145: distGeomHelpersCatch 145: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 145: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 145: Test timeout computed to be: 1500 -126/230 Test #137: pyMolTransforms ........................ Passed 1.39 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +144: [17:55:00] ******************************************************** +144: [17:55:00] Testing DistGeomHelpers +144: [17:55:00] --------------------------------- +144: [17:55:00] test2 +144: +144: go +144: ------------------------------------- +144: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: =>start test rdf +116: [17:55:00] test on : 365 molecules done +104/230 Test #116: testRDF ................................ Passed 0.62 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-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 146: Test timeout computed to be: 1500 -145: Randomness seeded to: 1882134578 -139: processing -139: launch :0 -139: launch :1 -139: launch :2 -139: launch :3 -139: [09:08:21] Rep: 0 Mol:1 -139: [09:08:21] Rep: 0 Mol:0 -139: [09:08:21] Rep: 0 Mol:3 -139: [09:08:21] Rep: 0 Mol:5 -145: [09:08:21] [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: [09:08:21] [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: [09:08:21] Rep: 0 Mol:2 -139: [09:08:21] Rep: 0 Mol:9 -145: [09:08:21] [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: [09:08:21] [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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [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)] -139: [09:08:21] Rep: 0 Mol:4 -139: [09:08:21] Rep: 0 Mol:13 -145: [09:08:21] [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: [09:08:21] [*: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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [$([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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] Rep: 0 Mol:17 -145: [09:08:21] 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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [$([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: [09:08:21] [$([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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [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: [09:08:21] [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: [09:08:21] 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: [09:08:21] 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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [!#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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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)] -139: [09:08:21] Rep: 0 Mol:8 -139: [09:08:21] Rep: 0 Mol:6 -145: [09:08:21] [$([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: [09:08:21] [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: [09:08:21] 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: [09:08:21] Rep: 0 Mol:12 -139: [09:08:21] Rep: 0 Mol:10 -145: ----------- -139: [09:08:21] Rep: 0 Mol:21 -145: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [$(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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] [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: [09:08:21] Rep: 0 Mol:25 -139: [09:08:21] Rep: 0 Mol:16 -139: [09:08:21] Rep: 0 Mol:29 -139: [09:08:21] Rep: 0 Mol:7 -139: [09:08:21] Rep: 0 Mol:11 -139: [09:08:21] Rep: 0 Mol:15 -139: [09:08:21] Rep: 0 Mol:20 -139: [09:08:21] Rep: 0 Mol:19 -139: [09:08:21] Rep: 0 Mol:23 -139: [09:08:21] Rep: 0 Mol:27 -139: [09:08:21] Rep: 0 Mol:31 -139: [09:08:21] Rep: 0 Mol:24 -139: [09:08:21] Rep: 0 Mol:28 -139: [09:08:21] Rep: 0 Mol:14 -139: [09:08:21] Rep: 0 Mol:18 -139: [09:08:21] Rep: 0 Mol:22 -139: [09:08:21] Rep: 0 Mol:26 -145: [09:08:21] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -139: [09:08:21] Rep: 0 Mol:30 -145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 -145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 -124: Warning: Atom Count for residue LYS80A does not match expected count -145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 1 -139: [09:08:21] Rep: 20 Mol:1 -139: [09:08:21] Rep: 20 Mol:5 -139: [09:08:21] Rep: 20 Mol:9 -139: [09:08:21] Rep: 20 Mol:13 -139: [09:08:21] Rep: 20 Mol:17 -139: [09:08:21] Rep: 20 Mol:21 -139: [09:08:21] Rep: 20 Mol:25 -139: [09:08:21] Rep: 20 Mol:29 -143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:21] Rep: 20 Mol:2 -139: [09:08:21] Rep: 20 Mol:6 -139: [09:08:21] Rep: 20 Mol:10 -141: processing -141: launch :0 -141: launch :1 -141: launch :2 -141: launch :3 -141: [09:08:21] Rep: 0 Mol:2 -139: [09:08:21] Rep: 20 Mol:14 -139: [09:08:21] Rep: 20 Mol:18 -139: [09:08:21] Rep: 20 Mol:22 -139: [09:08:21] Rep: 20 Mol:26 -139: [09:08:21] Rep: 20 Mol:30 -143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:21] Rep: 0 Mol:1 -141: [09:08:21] Rep: 0 Mol:0 -141: [09:08:21] Rep: 0 Mol:3 -143: ..[09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [09:08:21] Rep: 0 Mol:5 -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:21] Rep: 0 Mol:9 -141: [09:08:21] Rep: 0 Mol:4 -120: =>start test GETAWAY -120: [09:08:21] test on : 365 molecules done -141: [09:08:21] Rep: 0 Mol:6 -141: [09:08:21] Rep: 0 Mol:13 -127/230 Test #120: testGETAWAY ............................ Passed 4.11 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing Issue239. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: Randomness seeded to: 2512619256 +68: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [17:55:00] deprecated group abbreviation ignored on line 24 +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +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: [17:55:00] +68: +68: **** +113: [17:55:00] 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: [17:55:00] initialization failed +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0x00007F043E8C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0x00007F043E8D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# 0x00007F043E8D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 6# 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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 9# 0x000056043CA0CCF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x000056043CA734F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0x000056043C9F3963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 12# 0x00007F043DE33D68 in /lib/x86_64-linux-gnu/libc.so.6 +68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +68: 14# 0x000056043C9F3B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing calcEnergy with passed coords. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test unfolded version of RDKFP +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test topological torsion fp generator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +121: =>start test autocorr3D +121: [17:55:00] test on : 365 molecules done +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing calcGrad. +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/230 Test #121: testAUTOCORR3D ......................... Passed 0.51 sec test 147 Start 147: testMolAlign 147: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 147: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 147: Test timeout computed to be: 1500 -141: [09:08:21] Rep: 0 Mol:10 -141: [09:08:21] Rep: 0 Mol:7 -141: [09:08:21] Rep: 0 Mol:11 -141: [09:08:21] Rep: 0 Mol:8 -141: [09:08:21] Rep: 0 Mol:15 -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test Issue252: Bad definitions for Crippen atom types. -141: [09:08:21] Rep: 0 Mol:17 -143: .[09:08:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:21] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:21] Rep: 0 Mol:12 -141: [09:08:21] Rep: 0 Mol:16 -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test calculation of ChiVs. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test calculation of ChiNs. -141: [09:08:21] Rep: 0 Mol:19 -141: [09:08:21] Rep: 0 Mol:23 -141: [09:08:21] Rep: 0 Mol:27 -141: [09:08:21] Rep: 0 Mol:20 -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test calculation of HallKierAlpha. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test calculation of Kappa1. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -141: [09:08:21] Rep: 0 Mol:24 -141: [09:08:21] Rep: 0 Mol:31 -109: [09:08:21] Test calculation of Kappa2. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test calculation of Kappa3. -141: [09:08:21] Rep: 0 Mol:28 -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test Crippen atom type calculations. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test ring descriptors -145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 5 -141: [09:08:21] Rep: 0 Mol:14 -139: [09:08:21] Rep: 20 Mol:3 -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test other count descriptors. -109: [09:08:21] done -109: [09:08:21] ------------------------------------- -109: [09:08:21] Test MQN -145: [09:08:21] UFFTYPER: Unrecognized charge state for atom: 5 -141: [09:08:22] Rep: 0 Mol:18 -139: [09:08:22] Rep: 20 Mol:7 -139: [09:08:22] Rep: 20 Mol:11 -139: [09:08:22] Rep: 20 Mol:15 -139: [09:08:22] Rep: 20 Mol:19 -139: [09:08:22] Rep: 20 Mol:23 -139: [09:08:22] Rep: 20 Mol:27 -139: [09:08:22] Rep: 20 Mol:31 -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test GitHub Issue 56. -109: [09:08:22] WARNING: not removing hydrogen atom without neighbors -109: [09:08:22] WARNING: not removing hydrogen atom without neighbors -109: [09:08:22] WARNING: not removing hydrogen atom without neighbors -109: [09:08:22] WARNING: not removing hydrogen atom without neighbors -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github92: Bad Crippen atom type for pyrrole H. -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github362: order dependence in Kier-Hall descriptors. -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test calculation of spiro and bridgehead counts. -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github694: ExactMolWt ignoring the mass of the electron -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Testing Properties and KitchenSink -141: [09:08:22] Rep: 0 Mol:21 -109: [09:08:22] ---Caught keyerror (bad property name)--- -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test USR Descriptor -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github #1973: support P and S terms for TPSA calculation -141: [09:08:22] Rep: 0 Mol:22 -109: [09:08:22] done -109: [09:08:22] ------------------------------------- -109: [09:08:22] Test Github #2948: Empty molecule has non-zero LabuteASA -109: [09:08:22] done -128/230 Test #109: testDescriptors ........................ Passed 6.27 sec +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [17:55:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: Elapsed time: 0.671131 s +113: Errors:0 +113: [17:55:00] test on : 500 molecules done +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +106/230 Test #113: testEEM ................................ Passed 0.70 sec test 148 Start 148: testO3AAlign 148: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 148: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 148: Test timeout computed to be: 1500 -141: [09:08:22] Rep: 0 Mol:26 -141: [09:08:22] Rep: 0 Mol:25 -145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 5 -146: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:22] Rep: 0 Mol:30 -141: [09:08:22] Rep: 0 Mol:29 -139: [09:08:22] Rep: 20 Mol:0 -139: [09:08:22] Rep: 20 Mol:4 -139: [09:08:22] Rep: 20 Mol:8 -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 20 Mol:12 -139: [09:08:22] Rep: 20 Mol:16 -139: [09:08:22] Rep: 20 Mol:20 -139: [09:08:22] Rep: 20 Mol:24 -139: [09:08:22] Rep: 20 Mol:28 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -123: Warning: Atom Count for residue GLU150A does not match expected count -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: ..[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:1 -139: [09:08:22] Rep: 40 Mol:5 -139: [09:08:22] Rep: 40 Mol:9 -145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 -87: [09:08:22] Explicit valence for atom # 9 N, 6, is greater than permitted -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:13 -139: [09:08:22] Rep: 40 Mol:17 -139: [09:08:22] Rep: 40 Mol:21 -139: [09:08:22] Rep: 40 Mol:25 -139: [09:08:22] Rep: 40 Mol:29 -146: ..[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 -146: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [09:08:22] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: *********************************************************** -147: Testing MolAlign -147: --------------------------------- -147: test1MolAlign -147: -147: --------------------------------- -147: test1GetBestRMS -147: -147: --------------------------------- -147: test1MolWithQueryAlign -147: -147: --------------------------------- -147: test2AtomMap -147: -147: --------------------------------- -147: test3Weights -147: -147: --------------------------------- -147: testIssue241 -147: -147: *********************************************************** -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: ...[09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -145: [09:08:22] UFFTYPER: Unrecognized charge state for atom: 6 -129/230 Test #147: testMolAlign ........................... Passed 0.33 sec +128: [17:55:00] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Topological Torsions. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Folded torsions. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Bulk Topological Torsions. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] PMI edge cases. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] NPR edge cases. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] 3D descriptors. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] 3D descriptor edge cases. +118: [17:55:00] done +118: [17:55:00] ------------------------------------- +118: [17:55:00] Inertial shape factor. +118: [17:55:00] done +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing Issue242. +107/230 Test #118: test3D ................................. Passed 0.63 sec test 149 Start 149: molAlignCatchTest 149: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 149: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -123: Warning: Atom Count for residue ASN157A does not match expected count -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -143: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -149: Randomness seeded to: 2176915630 -149: 93522919 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:3 -139: [09:08:22] Rep: 40 Mol:7 -139: [09:08:22] Rep: 40 Mol:11 -139: [09:08:22] Rep: 40 Mol:15 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:19 -139: [09:08:22] Rep: 40 Mol:23 -139: [09:08:22] Rep: 40 Mol:27 -139: [09:08:22] Rep: 40 Mol:31 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:2 -139: [09:08:22] Rep: 40 Mol:6 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:10 -139: [09:08:22] Rep: 40 Mol:14 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:18 -139: [09:08:22] Rep: 40 Mol:22 -139: [09:08:22] Rep: 40 Mol:26 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:30 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -149: 109508588 -143: ... -143: ---------------------------------------------------------------------- -143: Ran 19 tests in 0.729s -143: -143: OK -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 60 Mol:1 -139: [09:08:22] Rep: 60 Mol:5 -139: [09:08:22] Rep: 60 Mol:9 -139: [09:08:22] Rep: 60 Mol:13 -139: [09:08:22] Rep: 60 Mol:17 -139: [09:08:22] Rep: 60 Mol:21 -139: [09:08:22] Rep: 60 Mol:25 -139: [09:08:22] Rep: 60 Mol:29 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:0 -139: [09:08:22] Rep: 40 Mol:4 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 40 Mol:8 -139: [09:08:22] Rep: 40 Mol:12 -139: [09:08:22] Rep: 40 Mol:16 -139: [09:08:22] Rep: 40 Mol:20 -139: [09:08:22] Rep: 40 Mol:24 -139: [09:08:22] Rep: 40 Mol:28 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:22] Rep: 100 Mol:3 -141: [09:08:22] Rep: 100 Mol:7 -141: [09:08:22] Rep: 100 Mol:11 -141: [09:08:22] Rep: 100 Mol:15 -141: [09:08:22] Rep: 100 Mol:19 -141: [09:08:22] Rep: 100 Mol:23 -141: [09:08:22] Rep: 100 Mol:27 -141: [09:08:22] Rep: 100 Mol:31 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:22] Rep: 60 Mol:3 -139: [09:08:22] Rep: 60 Mol:7 -139: [09:08:22] Rep: 60 Mol:11 -139: [09:08:22] Rep: 60 Mol:15 -139: [09:08:22] Rep: 60 Mol:19 -139: [09:08:22] Rep: 60 Mol:23 -139: [09:08:22] Rep: 60 Mol:27 -139: [09:08:22] Rep: 60 Mol:31 -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:22] Molecule does not have explicit Hs. Consider calling AddHs() -130/230 Test #143: pyForceFieldHelpers .................... Passed 2.22 sec +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: Test +67: +67: NewChiralTest +67: +67: Test +67: +67: NewChiralTestNoChiral +67: +67: Test +67: +67: NewChiralTestNoChiral +67: +67: Test +67: +67: NewChiralTest2 +67: +67: Test +67: +67: NewChiralTest2 +67: +67: Test +67: +67: NewChiralTest2AllChiral +67: +67: Test +67: +67: NewChiralTest2AllChiral +67: +67: Test +67: +67: Vendor839 +67: +67: Test +67: +67: DoubleBondChain +67: +67: Test +67: +67: Na_Mg_Al_OH +67: +67: Test +67: +67: Pb +67: +67: Test +67: +67: O_Mg_Si +67: +67: Test +67: +67: SquiggleBond +67: +67: Test +67: +67: BigMacrocycle +67: +67: Test +67: +67: Smiles1 +67: +123: Warning: Atom Count for residue ASN39A does not match expected count +108/230 Test #67: testMrvToMol ........................... Passed 0.98 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-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 150: Test timeout computed to be: 1500 -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:23] Rep: 80 Mol:1 -139: [09:08:23] Rep: 80 Mol:5 -139: [09:08:23] Rep: 80 Mol:9 -139: [09:08:23] Rep: 80 Mol:13 -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:23] Rep: 100 Mol:0 -139: [09:08:23] Rep: 80 Mol:17 -139: [09:08:23] Rep: 80 Mol:21 -139: [09:08:23] Rep: 80 Mol:25 -141: [09:08:23] Rep: 100 Mol:4 -141: [09:08:23] Rep: 100 Mol:8 -141: [09:08:23] Rep: 100 Mol:12 -141: [09:08:23] Rep: 100 Mol:16 -141: [09:08:23] Rep: 100 Mol:20 -141: [09:08:23] Rep: 100 Mol:24 -139: [09:08:23] Rep: 80 Mol:29 -141: [09:08:23] Rep: 100 Mol:28 -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -87: [09:08:23] Explicit valence for atom # 3 Al, 6, is greater than permitted -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:23] Rep: 60 Mol:2 -139: [09:08:23] Rep: 60 Mol:6 -139: [09:08:23] Rep: 60 Mol:10 -139: [09:08:23] Rep: 60 Mol:14 -139: [09:08:23] Rep: 60 Mol:18 -139: [09:08:23] Rep: 60 Mol:22 -139: [09:08:23] Rep: 60 Mol:26 -139: [09:08:23] Rep: 60 Mol:30 -146: .[09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:23] Rep: 100 Mol:2 -141: [09:08:23] Rep: 100 Mol:6 -141: [09:08:23] Rep: 100 Mol:10 -141: [09:08:23] Rep: 100 Mol:14 -141: [09:08:23] Rep: 100 Mol:18 -141: [09:08:23] Rep: 100 Mol:22 -141: [09:08:23] Rep: 100 Mol:26 -141: [09:08:23] Rep: 100 Mol:30 -139: [09:08:23] Rep: 80 Mol:3 -139: [09:08:23] Rep: 80 Mol:7 -139: [09:08:23] Rep: 80 Mol:11 -139: [09:08:23] Rep: 80 Mol:15 -139: [09:08:23] Rep: 80 Mol:19 -139: [09:08:23] Rep: 80 Mol:23 -139: [09:08:23] Rep: 80 Mol:27 -139: [09:08:23] Rep: 80 Mol:31 -87: [09:08:23] Explicit valence for atom # 4 Al, 6, is greater than permitted -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -139: [09:08:23] Rep: 60 Mol:0 -139: [09:08:23] Rep: 60 Mol:4 -141: [09:08:23] Rep: 100 Mol:1 -141: [09:08:23] Rep: 100 Mol:5 -141: [09:08:23] Rep: 100 Mol:9 -141: [09:08:23] Rep: 100 Mol:13 -141: [09:08:23] Rep: 100 Mol:17 -141: [09:08:23] Rep: 100 Mol:21 -141: [09:08:23] Rep: 100 Mol:25 -141: [09:08:23] Rep: 100 Mol:29 -139: [09:08:23] Rep: 60 Mol:8 -139: [09:08:23] Rep: 60 Mol:12 -139: [09:08:23] Rep: 60 Mol:16 -139: [09:08:23] Rep: 60 Mol:20 -139: [09:08:23] Rep: 60 Mol:24 -139: [09:08:23] Rep: 60 Mol:28 -124: Warning: Atom Count for residue GLU150A does not match expected count -87: [09:08:23] Explicit valence for atom # 10 Si, 6, is greater than permitted -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -124: Warning: Atom Count for residue ASN157A does not match expected count -139: [09:08:23] Rep: 80 Mol:0 -139: [09:08:23] Rep: 80 Mol:4 -139: [09:08:23] Rep: 80 Mol:8 -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -139: [09:08:23] Rep: 80 Mol:12 -139: [09:08:23] Rep: 80 Mol:16 -139: [09:08:23] Rep: 80 Mol:20 -139: [09:08:23] Rep: 80 Mol:24 -139: [09:08:23] Rep: 80 Mol:28 -139: [09:08:23] Rep: 80 Mol:2 -139: [09:08:23] Rep: 80 Mol:6 -139: [09:08:23] Rep: 80 Mol:10 -139: [09:08:23] Rep: 80 Mol:14 -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -139: [09:08:23] Rep: 80 Mol:18 -139: [09:08:23] Rep: 80 Mol:22 -139: [09:08:23] Rep: 80 Mol:26 -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -139: [09:08:23] Rep: 80 Mol:30 -145: [09:08:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -146: [09:08:23] Molecule does not have explicit Hs. Consider calling AddHs() -149: 1411383903 -27: All 191 tests passed -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -139: [09:08:24] done -139: [09:08:24] ------------------------------------- -139: [09:08:24] Test MMFF multithreading2 -144: [09:08:20] --------------------------------- -144: [09:08:20] test3 -144: -144: [09:08:20] --------------------------------- -144: [09:08:20] test4 -144: -144: [09:08:20] --------------------------------- -144: [09:08:20] test5 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test6 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test15Dists -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test Issue 215 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testMultipleConfs -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testMultipleConfsExpTors -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue227 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue236 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testOrdering -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue244 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue251 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue276 -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue284 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue285 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testIssue355 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] testRandomCoords -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 1989539 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 2091864 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test constrained embedding -144: -144: [09:08:24] ssd: 0.0752641 -144: [09:08:24] ssd: 0.0659363 -146: [09:08:24] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:24] done -141: [09:08:24] ------------------------------------- -141: [09:08:24] Test UFF multithreading2 -87: [09:08:24] Explicit valence for atom # 2 O, 4, is greater than permitted -149: 878192114 -149: =============================================================================== -149: All tests passed (73 assertions in 3 test cases) -149: -131/230 Test #149: molAlignCatchTest ...................... Passed 2.68 sec +145: [17:55:00] [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: [17:55:00] [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: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing github 308: crash during MMFF parameterization . +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing SFIssue1653802. +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Testing SFIssue2378119. +139: [17:55:00] done +139: [17:55:00] ------------------------------------- +139: [17:55:00] Test MMFF force-field parameter getters. +145: [17:55:00] [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: [17:55:00] [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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +139: [17:55:00] ------------------------------------- +139: [17:55:00] Test MMFF multithreading +145: [17:55:00] [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)] +109/230 Test #142: testCrystalForceField .................. Passed 0.19 sec test 151 Start 151: testFeatures 151: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 151: Test timeout computed to be: 1500 -151: [09:08:24] ------------------------------------- -151: [09:08:24] AtomType parser testing. -151: [09:08:24] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -151: [09:08:24] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -151: [09:08:24] done -151: [09:08:24] ------------------------------------- -151: [09:08:24] FeatureDefinition parser testing. -151: [09:08:24] done -151: [09:08:24] ------------------------------------- -151: [09:08:24] Test pulling feat defs from a string. -151: [09:08:24] done -151: [09:08:24] ------------------------------------- -151: [09:08:24] FeatureDef functionality testing. -87: [09:08:24] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [09:08:24] Explicit valence for atom # 3 Be, 4, is greater than permitted -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] FeatureFactory testing. -151: [09:08:25] 1 -151: [09:08:25] 2 -151: [09:08:25] 3 -151: [09:08:25] 4 -151: [09:08:25] 5 -151: [09:08:25] 6 -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Feature Location testing. -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Test building a FeatureFactory from a file -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing Issue 224. -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing Issue 225. -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Test Issue346 -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Test Issue347 -151: [09:08:25] done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing Issue 348. -151: [09:08:25] SMARTS Parse Error: syntax error while parsing: [C[C] -151: [09:08:25] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing Nested AtomType definitions. +145: [17:55:00] [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: [17:55:00] [*: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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [$([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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] 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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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)] +139: generating reference data +145: [17:55:00] [$([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: [17:55:00] [$([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: [17:55:00] [$(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: [17:55:00] [$(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: [17:55:00] [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: [17:55:00] [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)] +151: [17:55:00] ------------------------------------- +151: [17:55:00] AtomType parser testing. +145: [17:55:00] 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: [17:55:00] 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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [!#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: [17:55:00] [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: [17:55:00] [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: ----------- +151: [17:55:00] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +151: [17:55:00] 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: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] FeatureDefinition parser testing. +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Test pulling feat defs from a string. +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] FeatureDef functionality testing. +145: [17:55:00] [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: [17:55:00] [$([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: [17:55:00] [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: [17:55:00] 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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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)] +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] FeatureFactory testing. +145: [17:55:00] [$(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)] +151: [17:55:00] 1 +151: [17:55:00] 2 +151: [17:55:00] 3 +151: [17:55:00] 4 +151: [17:55:00] 5 +151: [17:55:00] 6 +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Feature Location testing. +145: [17:55:00] [$(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: [17:55:00] [$(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)] +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Test building a FeatureFactory from a file +145: [17:55:00] [$(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: [17:55:00] [$(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)] +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing Issue 224. +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing Issue 225. +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Test Issue346 +145: [17:55:00] [$(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)] +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Test Issue347 +151: [17:55:00] done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing Issue 348. +151: [17:55:00] SMARTS Parse Error: syntax error while parsing: [C[C] +151: [17:55:00] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing Nested AtomType definitions. 151: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing Github Issue #252: crash when calling getPos() with no conformer. -151: [09:08:25] expect a precondition failure message below -151: [09:08:25] +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing Github Issue #252: crash when calling getPos() with no conformer. +151: [17:55:00] expect a precondition failure message below +151: [17:55:00] 151: 151: **** 151: Pre-condition Violation @@ -27803,403 +26640,468 @@ 151: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 151: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 151: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -151: 4# 0x0000559F1AFA0E20 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 5# 0x0000559F1AF956A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 6# 0x00007F488C031D68 in /lib/x86_64-linux-gnu/libc.so.6 +151: 4# 0x000055D63076CE20 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 5# 0x000055D6307616A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 6# 0x00007F0208E33D68 in /lib/x86_64-linux-gnu/libc.so.6 151: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -151: 8# 0x0000559F1AF957A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 8# 0x000055D6307617A1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: ---------- 151: **** 151: -151: [09:08:25] Done -151: [09:08:25] ------------------------------------- -151: [09:08:25] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -151: [09:08:25] done -132/230 Test #151: testFeatures ........................... Passed 0.08 sec +151: [17:55:00] Done +151: [17:55:00] ------------------------------------- +151: [17:55:00] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +151: [17:55:00] done +145: [17:55:00] [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)] +110/230 Test #151: testFeatures ........................... Passed 0.04 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-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 152: Test timeout computed to be: 1500 -87: [09:08:25] Explicit valence for atom # 27 P, 6, is greater than permitted -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 2091974 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 2835784 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 3019283 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 3238580 -144: -144: [09:08:24] --------------------------------- -144: [09:08:24] test sf.net issue 3483968 -144: -144: [09:08:25] --------------------------------- -144: [09:08:25] test github issue 55 -144: -144: [09:08:25] --------------------------------- -144: [09:08:25] test1 -144: -144: [09:08:25] --------------------------------- -144: [09:08:25] test multi-threading -144: -144: building molecules -152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() -144: generating reference data -152: ..[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() -87: =============================================================================== -87: All tests passed (21162 assertions in 3 test cases) -87: -152: .[09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[09:08:25] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -152: [09:08:25] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -152: ... -152: ---------------------------------------------------------------------- -152: Ran 9 tests in 0.124s -152: -152: OK -133/230 Test #87: multithreadedSupplierCatchTest ......... Passed 11.23 sec +145: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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: [17:55:00] [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)] +87: [17:55:00] Explicit valence for atom # 2 O, 4, is greater than permitted +131: .............. +131: ---------------------------------------------------------------------- +131: Ran 14 tests in 0.116s +131: +131: OK +126: pass 2 +126: launch :0 +126: launch :1 +126: launch :2 +126: launch :3 +34: [17:55:00] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +107: [17:55:00] +107: +107: **** +107: Invariant Violation +107: nonsense +107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +107: Failed Expression: token != tokens.end() +107: ---------- +107: Stacktrace: +107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 2# 0x00007FB689A02EFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 4# 0x00005617FEA7F183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x00005617FEA7C731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x00007FB688C33D68 in /lib/x86_64-linux-gnu/libc.so.6 +107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +107: 8# 0x00005617FEA7C861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: ---------- +107: **** +107: +107: [17:55:00] +107: +107: **** +107: Invariant Violation +107: nonsense no new line +107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +107: Failed Expression: token != tokens.end() +107: ---------- +107: Stacktrace: +107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 2# 0x00007FB689A02EFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 4# 0x00005617FEA7F183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x00005617FEA7C731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x00007FB688C33D68 in /lib/x86_64-linux-gnu/libc.so.6 +107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +107: 8# 0x00005617FEA7C861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: ---------- +107: **** +107: +107: [17:55:00] +107: +107: **** +107: Invariant Violation +107: nonsense with tab +107: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +107: Failed Expression: token != tokens.end() +107: ---------- +107: Stacktrace: +107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +107: 2# 0x00007FB689A02EFD in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 4# 0x00005617FEA7F183 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x00005617FEA7C731 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x00007FB688C33D68 in /lib/x86_64-linux-gnu/libc.so.6 +107: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +107: 8# 0x00005617FEA7C861 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: ---------- +107: **** +107: +125: ........ +125: ---------------------------------------------------------------------- +125: Ran 8 tests in 0.207s +125: +125: OK +111/230 Test #107: testFragCatalog ........................ Passed 0.88 sec test 153 Start 153: testShapeHelpers 153: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 153: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 153: Test timeout computed to be: 1500 -139: [09:08:25] done -139: [09:08:25] ------------------------------------- -139: [09:08:25] Test MMFF multithreading3 -153: *********************************************************** -153: Testing ShapeHelpers -153: --------------------------------- -153: test1Encode -153: -153: --------------------------------- -153: test2Compare -153: -153: --------------------------------- -153: testGithub4364 -153: -153: *********************************************************** -134/230 Test #153: testShapeHelpers ....................... Passed 0.09 sec +117: =>start test MORSE +117: =>read file +117: [17:55:00] test on : 365 molecules done +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing UFF special cases. +141: [17:55:00] UFFTYPER: Unrecognized charge state for atom: 0 +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing Issue239. +140: done +137: ........ +137: ---------------------------------------------------------------------- +137: Ran 8 tests in 0.034s +137: +137: OK +87: [17:55:00] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [17:55:00] Explicit valence for atom # 3 Be, 4, is greater than permitted +112/230 Test #117: testMORSE .............................. Passed 0.78 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-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 154: Test timeout computed to be: 1500 -135/230 Test #152: pyChemicalFeatures ..................... Passed 0.70 sec +132: .. +132: ---------------------------------------------------------------------- +132: Ran 2 tests in 0.037s +132: +132: OK +68: [17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [17:55:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +140: [17:55:00] done +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing calcEnergy with passed coords. +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 +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Rooted Topological Torsions. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test ignoring atoms in Topological Torsions. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +141: [17:55:00] done +141: [17:55:00] ------------------------------------- +141: [17:55:00] Testing calcGrad. +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test Topological Torsions including info about chirality. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +149: Randomness seeded to: 1489175183 +149: 59527879 +128: [17:55:00] done +128: [17:55:00] ------------------------------------- +128: [17:55:00] Test convenience and bulk fp calculation functions +34: [17:55:01] ----------------------- +34: Testing isRingFused +141: [17:55:01] done +141: [17:55:01] ------------------------------------- +141: [17:55:01] Testing SFIssue1653802. +141: [17:55:01] done +141: [17:55:01] ------------------------------------- +141: [17:55:01] Testing SFIssue2378119. +87: [17:55:01] Explicit valence for atom # 27 P, 6, is greater than permitted +141: [17:55:01] done +141: [17:55:01] ------------------------------------- +141: [17:55:01] Test UFF force-field parameter getters. +141: [17:55:01] ------------------------------------- +141: [17:55:01] Testing handling missing parameters. +113/230 Test #34: graphmolMolOpsTest ..................... Passed 1.23 sec test 155 Start 155: testMolCatalog 155: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 155: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 155: Test timeout computed to be: 1500 -136/230 Test #155: testMolCatalog ......................... Passed 0.05 sec +141: [17:55:01] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [17:55:01] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [17:55:01] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [17:55:01] UFFTYPER: Unrecognized atom type: Cu+1 (0) +153: *********************************************************** +153: Testing ShapeHelpers +153: --------------------------------- +153: test1Encode +153: +153: --------------------------------- +153: test2Compare +153: +153: --------------------------------- +153: testGithub4364 +153: +153: *********************************************************** +123: Warning: Atom Count for residue GLU53A does not match expected count +114/230 Test #125: pyMolDescriptors3D ..................... Passed 0.62 sec +115/230 Test #153: testShapeHelpers ....................... 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-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 156: Test timeout computed to be: 1500 -146: [09:08:25] Molecule does not have explicit Hs. Consider calling AddHs() -141: [09:08:26] done -141: [09:08:26] ------------------------------------- -141: [09:08:26] Test UFF multithreading3 -146: [09:08:26] Molecule does not have explicit Hs. Consider calling AddHs() -115: =>start test GETAWAY custom -115: [09:08:26] test on : 365 molecules done -137/230 Test #115: testRDFcustom .......................... Passed 9.77 sec test 157 Start 157: moldraw2DTest1 157: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 157: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 157: Test timeout computed to be: 1500 -157: ----------------- Test 1 -157: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -157: Done -157: ----------------- Test 2 -157: file test2_1.png gave hash 2445376551U not the expected 307437906U -157: file test2_2.png gave hash 1007500626U not the expected 610424244U -157: Done -157: ----------------- Test 4 -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -157: file test4_1.png gave hash 2289651897U not the expected 1403972924U -157: Done -157: ----------------- Test 5 -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Test unfolded version of RDKFP -126: [09:08:26] ------------------------------------- -126: [09:08:26] 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: [09:08:26] ------------------------------------- -126: [09:08:26] Single atoms setting radius 1 bits in Morgan fingerprints -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #879: Pattern fingerprint should set bits for single-atom fragments. -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use AtomPairGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #2115: BitInfo not complete for RDKFingerprint -126: [09:08:26] done -126: [09:08:26] ------------------------------------- -126: [09:08:26] Github #3723: Fingerprint crash for mols with Zero order bonds -126: [09:08:26] done -138/230 Test #126: testFingerprints ....................... Passed 8.14 sec +141: [17:55:01] done +141: [17:55:01] ------------------------------------- +141: [17:55:01] Testing SFIssue3009337. +141: [17:55:01] done +141: [17:55:01] ------------------------------------- +141: [17:55:01] Test UFF multithreading +147: *********************************************************** +147: Testing MolAlign +147: --------------------------------- +147: test1MolAlign +147: +147: --------------------------------- +147: test1GetBestRMS +147: +147: --------------------------------- +147: test1MolWithQueryAlign +147: +147: --------------------------------- +147: test2AtomMap +147: +147: --------------------------------- +147: test3Weights +147: +147: --------------------------------- +147: testIssue241 +147: +147: *********************************************************** +116/230 Test #131: pyTestGenerator ........................ Passed 0.54 sec +117/230 Test #132: pyTestMHFP ............................. Passed 0.50 sec +118/230 Test #137: pyMolTransforms ........................ Passed 0.43 sec +119/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.39 sec +120/230 Test #147: testMolAlign ........................... Passed 0.20 sec +121/230 Test #155: testMolCatalog ......................... Passed 0.03 sec test 158 Start 158: moldraw2DTestCatch 158: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 158: Test timeout computed to be: 1500 -154: . -154: ---------------------------------------------------------------------- -154: Ran 1 test in 0.206s -154: -154: OK -154: Testing Shape Helpers wrapper -157: file test5_1.png gave hash 1708884460U not the expected 1269428339U -157: file test5_2.png gave hash 263952708U not the expected 3073694291U -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.016s -156: -156: OK -157: file test5_3.png gave hash 2875214783U not the expected 1865192682U -139: [09:08:26] done -139: [09:08:26] ------------------------------------- -139: [09:08:26] Testing github 162: Incorrect SMILES after MMFF parameterization . -139: [09:08:26] done -139: [09:08:26] ------------------------------------- -139: [09:08:26] Testing github 224: crash during MMFF parameterization . -139: [09:08:26] done -139: [09:08:26] ------------------------------------- -139: [09:08:26] Testing github6728: crash due to missing stretch-bend params. -158: Randomness seeded to: 1047875229 -158: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -157: Done -157: ----------------- Test 6 (atom labels) -139/230 Test #139: testMMFFForceFieldHelpers .............. Passed 6.85 sec test 159 Start 159: moldraw2DRxnTest1 159: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -157: Done -157: ----------------- Test 7 (backgrounds) -140/230 Test #154: pyShapeHelpers ......................... Passed 1.23 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-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 160: Test timeout computed to be: 1500 -157: file test7_1.png gave hash 2503310706U not the expected 3033050306U -141/230 Test #156: pyMolCatalog ........................... Passed 1.17 sec test 161 Start 161: testFMCS 161: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 161: Test timeout computed to be: 1500 -159: ----------------- Test 1 -157: file test7_2.png gave hash 4294114077U not the expected 3476380724U -157: Done -157: ----------------- Test8: PrepareMolDrawing -157: Done -157: ----------------- Test multi-threaded drawing -157: reading molecules -73: [09:08:26] Finished: testSmiCorrectness() -73: [09:08:26] ----------------------------------------- -73: -73: [09:08:26] -73: ----------------------------------------- -159: file rxn_test1_1.png gave hash 1238594098U not the expected 1556334749U -157: generating reference drawings -158: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U -159: file rxn_test1_2.png gave hash 2408715353U not the expected 1924084263U -73: [09:08:27] Spurious data before the first property will be ignored -73: [09:08:27] Property will be truncated after the first blank line -73: [09:08:27] Property will be truncated after the first blank line -73: [09:08:27] Property will be truncated after the first blank line -158: file contourMol_2.svg gave hash 4241964660U not the expected 572669511U -141: [09:08:27] done -141: [09:08:27] ------------------------------------- -141: [09:08:27] Testing GitHubIssue62. -158: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U -159: file rxn_test1_3.png gave hash 2702306328U not the expected 1644921059U -158: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U -141: [09:08:27] beta-lactam 39.6387 -141: [09:08:27] cyclopropanone 174.698 -141: [09:08:27] aziridine 337.986 -141: [09:08:27] aziridinone 115.248 -141: [09:08:27] isobutene 2.48217 -141: [09:08:27] acetone 1.91788 -158: file contourMol_5.svg gave hash 3954963517U not the expected 2230414999U -141: [09:08:27] cyclopentanone 10.1648 -141: [09:08:27] cyclopropene 99.4921 -141: [09:08:27] cyclobutene 41.0156 -141: [09:08:27] cyclopropane 267.236 -141: [09:08:27] gamma-lactam 15.7471 -159: file rxn_test1_4.png gave hash 1047103464U not the expected 2471435686U -141: [09:08:27] trans-2,3-diphenylcyclopropan-1-one 203.398 -159: file rxn_test1_5.png gave hash 867798763U not the expected 1428782307U -141: [09:08:27] cis-2,3-diphenylcyclopropan-1-one 206.852 -158: file testGithub3226_1.png gave hash 2960456425U not the expected 2350054896U -141: [09:08:27] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -141: [09:08:27] cyclopropylidencyclobutane 218.879 -159: file rxn_test1_6.png gave hash 3642317125U not the expected 483353696U -157: processing -157: launch :0 -157: launch :1 -157: launch :2 -157: launch :3 -158: file testGithub3226_2.png gave hash 903480972U not the expected 606206725U -141: [09:08:27] diphenylmethylidencyclobutane 79.6139 -141: [09:08:27] done -141: [09:08:27] ------------------------------------- -141: [09:08:27] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -141: [09:08:27] done -141: [09:08:27] ------------------------------------- -141: [09:08:27] Test square planar complexes -141: [09:08:27] done -141: [09:08:27] ------------------------------------- -141: [09:08:27] Test octahedral complexes -141: [09:08:27] done -142/230 Test #141: testUFFForceFieldHelpers ............... Passed 7.08 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-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 162: Test timeout computed to be: 1500 -158: file testGithub3226_3.png gave hash 1380525103U not the expected 2282880418U -159: file rxn_test1_7.png gave hash 1818284781U not the expected 528963379U -158: file testPNGMetadata_1.png gave hash 138627947U not the expected 2423299691U -159: file rxn_test1_7.svg gave hash 3432246161U not the expected 1389845691U -159: Done -159: ----------------- Test 2: some examples that caused problems in testing -159: file rxn_test2_1.png gave hash 1441990148U not the expected 399415052U -158: file testPNGMetadata_2.png gave hash 2913846030U not the expected 2803353117U -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 1239682505U not the expected 1215378243U -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 2733977819U not the expected 3645141778U -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 3575777004U not the expected 551946805U -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 -159: file rxn_test2_2_4.png gave hash 4049234447U not the expected 4234617566U -159: Done -159: ----------------- Test 3: test reactant highlighting -158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:27] 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 3887561208U not the expected 4176857511U -159: Done -159: ----------------- Test 4: some examples from SMARTS in testing -159: draw! -146: [09:08:27] Molecule does not have explicit Hs. Consider calling AddHs() -158: file testHandDrawn-1.png gave hash 3356982379U not the expected 698316547U -159: file rxn_test4_1.png gave hash 1743844008U not the expected 4187207676U -158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: done -158: file testHandDrawn-2.svg gave hash 1534109833U not the expected 4132716144U -158: [09:08:27] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:27] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-2.png gave hash 3620124651U not the expected 1605553248U -158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U -158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-3.png gave hash 1463224710U not the expected 2881952238U -158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U -158: [09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: file rxn_test4_2.png gave hash 2769144016U not the expected 3490081297U -158: file testHandDrawn-4.png gave hash 2460067691U not the expected 3431655453U -159: Done -143/230 Test #159: moldraw2DRxnTest1 ...................... Passed 1.28 sec test 163 Start 163: FMCStest 163: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 163: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 163: Test timeout computed to be: 1500 +141: generating reference data +145: [17:55:01] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 1 +149: 57073731 +68: ---------------------------------- +68: ---------------------------------- +68: [17:55:01] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +68: 3# 0x000056043CA1A0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x000056043CA7356A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x000056043C9F3963 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0x00007F043DE33D68 in /lib/x86_64-linux-gnu/libc.so.6 +68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +68: 8# 0x000056043C9F3B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +68: [17:55:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +134: ....... +134: ---------------------------------------------------------------------- +134: Ran 7 tests in 0.106s +134: +134: OK +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: ..[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 1 +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ..[17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: .[17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 1 +124: ..[17:55:01] +124: +124: **** +123: Warning: Atom Count for residue ARG64A does not match expected count +124: Pre-condition Violation +124: Number of atom props not equal to number of atoms +124: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp +124: Failed Expression: atom_props.size() == num_atoms +124: ---------- +124: Stacktrace: +124: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +124: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +124: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 +124: 3# 0x00007F3734E5A5D2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +124: 4# 0x00007F3734E6A256 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +124: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +124: 6# 0x00007F373936662C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +124: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +124: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +124: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +124: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +124: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +124: 12# 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-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +124: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +124: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +124: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +124: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 17# 0x00007F37369AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 18# 0x00007F37369AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 19# 0x00007F37369AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 20# 0x00007F37369AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 21# 0x00007F37369AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +124: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so +124: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so +124: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so +124: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so +124: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +124: 27# 0x00007F37393633C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +124: 28# _PyObject_MakeTpCall in /usr/bin/python3 +124: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 30# 0x0000000000546E76 in /usr/bin/python3 +124: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 32# _PyObject_Call_Prepend in /usr/bin/python3 +124: 33# 0x000000000059D6E4 in /usr/bin/python3 +124: 34# _PyObject_MakeTpCall in /usr/bin/python3 +124: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 36# 0x0000000000546E76 in /usr/bin/python3 +124: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 38# _PyObject_Call_Prepend in /usr/bin/python3 +124: 39# 0x000000000059D6E4 in /usr/bin/python3 +124: 40# _PyObject_MakeTpCall in /usr/bin/python3 +124: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 42# 0x0000000000546E76 in /usr/bin/python3 +124: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 44# _PyObject_Call_Prepend in /usr/bin/python3 +124: 45# 0x000000000059D6E4 in /usr/bin/python3 +124: 46# _PyObject_MakeTpCall in /usr/bin/python3 +124: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 48# _PyObject_Call_Prepend in /usr/bin/python3 +124: 49# 0x000000000059810D in /usr/bin/python3 +124: 50# 0x0000000000593E22 in /usr/bin/python3 +124: 51# _PyObject_MakeTpCall in /usr/bin/python3 +124: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 53# PyEval_EvalCode in /usr/bin/python3 +124: 54# 0x00000000005FFE7F in /usr/bin/python3 +124: 55# 0x00000000006A59F2 in /usr/bin/python3 +124: 56# _PyRun_SimpleFileObject in /usr/bin/python3 +124: 57# _PyRun_AnyFileObject in /usr/bin/python3 +124: 58# Py_RunMain in /usr/bin/python3 +124: 59# Py_BytesMain in /usr/bin/python3 +124: 60# 0x00007F3739B30D68 in /lib/x86_64-linux-gnu/libc.so.6 +124: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +124: 62# _start in /usr/bin/python3 +124: ---------- +124: **** +124: 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 @@ -29960,6 +28862,7 @@ 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 +157: ----------------- Test 1 163: 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 @@ -30165,114 +29068,341 @@ 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 163: ERROR: RDKit could not load input file -144/230 Test #163: FMCStest ............................... Passed 0.09 sec +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +159: ----------------- Test 1 +146: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: Randomness seeded to: 3365114252 +158: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +122/230 Test #134: pyPartialCharges ....................... Passed 0.59 sec +123/230 Test #163: FMCStest ............................... Passed 0.07 sec test 164 Start 164: molHashCatchTest 164: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 164: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 164: Test timeout computed to be: 1500 -160: ...[09:08:28] Font file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -160: [09:08:28] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -146: [09:08:28] Molecule does not have explicit Hs. Consider calling AddHs() -164: Randomness seeded to: 1788033641 -164: =============================================================================== -164: All tests passed (332 assertions in 13 test cases) -164: -145/230 Test #164: molHashCatchTest ....................... Passed 0.12 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-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 165: Test timeout computed to be: 1500 -160: ..........[09:08:28] -160: -160: **** -160: Pre-condition Violation -160: molecule must not be None -160: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -160: Failed Expression: m -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so -160: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so -160: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -160: 5# 0x00007FC28A37B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -160: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -160: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -160: 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -160: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -160: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -160: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -160: 12# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -160: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -160: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -160: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 16# 0x00007FC2899AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 17# 0x00007FC2899AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 18# 0x00007FC2899AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 19# 0x00007FC2899AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 20# 0x00007FC2899AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -160: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so -160: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so -160: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so -160: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so -160: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -160: 26# 0x00007FC28A3783C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -160: 27# _PyObject_MakeTpCall in /usr/bin/python3 -160: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 29# 0x0000000000546E76 in /usr/bin/python3 -160: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 31# _PyObject_Call_Prepend in /usr/bin/python3 -160: 32# 0x000000000059D6E4 in /usr/bin/python3 -160: 33# _PyObject_MakeTpCall in /usr/bin/python3 -160: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 35# 0x0000000000546E76 in /usr/bin/python3 -160: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 37# _PyObject_Call_Prepend in /usr/bin/python3 -160: 38# 0x000000000059D6E4 in /usr/bin/python3 -160: 39# _PyObject_MakeTpCall in /usr/bin/python3 -160: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 41# 0x0000000000546E76 in /usr/bin/python3 -160: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 43# _PyObject_Call_Prepend in /usr/bin/python3 -160: 44# 0x000000000059D6E4 in /usr/bin/python3 -160: 45# _PyObject_MakeTpCall in /usr/bin/python3 -160: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 47# _PyObject_Call_Prepend in /usr/bin/python3 -160: 48# 0x000000000059810D in /usr/bin/python3 -160: 49# 0x0000000000593E22 in /usr/bin/python3 -160: 50# _PyObject_MakeTpCall in /usr/bin/python3 -160: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -160: 52# PyEval_EvalCode in /usr/bin/python3 -160: 53# 0x00000000005FFE7F in /usr/bin/python3 -160: 54# 0x00000000006A59F2 in /usr/bin/python3 -160: 55# _PyRun_SimpleFileObject in /usr/bin/python3 -160: 56# _PyRun_AnyFileObject in /usr/bin/python3 -160: 57# Py_RunMain in /usr/bin/python3 -160: 58# Py_BytesMain in /usr/bin/python3 -160: 59# 0x00007FC28CBF1D68 in /lib/x86_64-linux-gnu/libc.so.6 -160: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -160: 61# _start in /usr/bin/python3 -160: ---------- -160: **** -160: -73: [09:08:28] Finished: testSDCorrectness() -73: [09:08:28] ----------------------------------------- -73: -146/230 Test #73: testMultithreadedMolSupplier ........... Passed 14.75 sec +124: ...Warning: Atom Count for residue GLU5A does not match expected count +124: Warning: Atom Count for residue ASN39A does not match expected count +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +157: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [17:55:01] UFFTYPER: Unrecognized atom type: Cu+1 (0) +157: Done +157: ----------------- Test 2 +124: Warning: Atom Count for residue GLU53A does not match expected count +124: Warning: Atom Count for residue ARG64A does not match expected count +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +124: Warning: Atom Count for residue LYS80A does not match expected count +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test2_1.png gave hash 2445376551U not the expected 307437906U +146: ..[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +106: .............[17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +124: Warning: Atom Count for residue GLU150A does not match expected count +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +124: Warning: Atom Count for residue ASN157A does not match expected count +143: ...[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U +157: file test2_2.png gave hash 1007500626U not the expected 610424244U +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +106: [17:55:01] SMILES Parse Error: syntax error while parsing: --- +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [17:55:01] dasfsadf +158: file contourMol_2.svg gave hash 4241964660U not the expected 572669511U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 5 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 5 +146: ..[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: Done +157: ----------------- Test 4 +158: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U +146: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 5 +158: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U +159: file rxn_test1_1.png gave hash 1238594098U not the expected 1556334749U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test4_1.png gave hash 2289651897U not the expected 1403972924U +157: Done +157: ----------------- Test 5 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file contourMol_5.svg gave hash 3954963517U not the expected 2230414999U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test5_1.png gave hash 1708884460U not the expected 1269428339U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test5_2.png gave hash 263952708U not the expected 3073694291U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test5_3.png gave hash 2875214783U not the expected 1865192682U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: Done +157: ----------------- Test 6 (atom labels) +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: Done +157: ----------------- Test 7 (backgrounds) +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +143: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testGithub3226_1.png gave hash 2960456425U not the expected 2350054896U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: file test7_1.png gave hash 2503310706U not the expected 3033050306U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testGithub3226_2.png gave hash 903480972U not the expected 606206725U +159: file rxn_test1_2.png gave hash 2408715353U not the expected 1924084263U +157: file test7_2.png gave hash 4294114077U not the expected 3476380724U +157: Done +157: ----------------- Test8: PrepareMolDrawing +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +157: Done +157: ----------------- Test multi-threaded drawing +157: reading molecules +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +123: Warning: Atom Count for residue LYS80A does not match expected count +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testGithub3226_3.png gave hash 1380525103U not the expected 2282880418U +164: Randomness seeded to: 3054385398 +164: =============================================================================== +164: All tests passed (332 assertions in 13 test cases) +164: +124/230 Test #164: molHashCatchTest ....................... Passed 0.14 sec test 166 Start 166: testMMPA 166: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 166: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 166: Test timeout computed to be: 1500 +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 6 +158: file testPNGMetadata_1.png gave hash 138627947U not the expected 2423299691U +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: All tests passed (2445 assertions in 29 test cases) +59: +125/230 Test #59: cxsmilesTest ........................... Passed 1.45 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-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +167: Test timeout computed to be: 1500 +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 6 +157: generating reference drawings +159: file rxn_test1_3.png gave hash 2702306328U not the expected 1644921059U +106: .[17:55:01] SMILES Parse Error: syntax error while parsing: mydoghasfleas +106: [17:55:01] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [17:55:01] Rep: 0 Mol:0 +141: [17:55:01] Rep: 0 Mol:3 +141: [17:55:01] Rep: 0 Mol:1 +141: [17:55:01] Rep: 0 Mol:5 +68: [17:55:01] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [17:55:01] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +141: [17:55:01] Rep: 0 Mol:2 +145: [17:55:01] UFFTYPER: Unrecognized charge state for atom: 6 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +141: [17:55:01] Rep: 0 Mol:9 +158: file testPNGMetadata_2.png gave hash 2913846030U not the expected 2803353117U +143: ... +143: ---------------------------------------------------------------------- +143: Ran 19 tests in 0.273s +143: +143: OK +141: [17:55:01] Rep: 0 Mol:4 +124: Warning: Atom Count for residue GLU5A does not match expected count +159: file rxn_test1_4.png gave hash 1047103464U not the expected 2471435686U +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.012s +156: +156: OK +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +141: [17:55:01] Rep: 0 Mol:7 +141: [17:55:01] Rep: 0 Mol:13 +128: [17:55:01] done +128: [17:55:01] ------------------------------------- +128: [17:55:01] Test GitHub Issue #6958 +128: [17:55:01] DEPRECATION WARNING: please use AtomPairGenerator +141: [17:55:01] Rep: 0 Mol:11 +126/230 Test #128: testFingerprintGenerators .............. Passed 0.91 sec +test 168 + Start 168: testRascalMCES + +168: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +168: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +168: Test timeout computed to be: 1500 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.005569 seconds +166: Time elapsed 0.009551 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 @@ -30289,8 +29419,14 @@ 166: 7: NOREF. Reference data NOT LISTED in test case. 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. +141: [17:55:01] Rep: 0 Mol:15 +141: [17:55:01] Rep: 0 Mol:6 +115: =>start test morse custom +115: [17:55:01] test on : 365 molecules done +152: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() 166: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 166: 9: NOREF. Reference data NOT LISTED in test case. +141: [17:55:01] Rep: 0 Mol:19 166: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 166: 10: NOREF. Reference data NOT LISTED in test case. 166: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] @@ -30301,19 +29437,36 @@ 166: 13: NOREF. Reference data NOT LISTED in test case. 166: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 166: 14: NOREF. Reference data NOT LISTED in test case. +159: file rxn_test1_5.png gave hash 867798763U not the expected 1428782307U 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. 166: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. +141: [17:55:01] Rep: 0 Mol:23 +141: [17:55:01] Rep: 0 Mol:27 166: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 166: 17: NOREF. Reference data NOT LISTED in test case. +141: [17:55:01] Rep: 0 Mol:10 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. +154: . +154: ---------------------------------------------------------------------- +154: Ran 1 test in 0.063s +154: +154: OK +154: Testing Shape Helpers wrapper +141: [17:55:01] Rep: 0 Mol:17 +68: [17:55:01] Empty atom list: 'M ALS 1 0 F' on line 8. +68: de_DE.UTF-8 +68: [17:55:01] ------------------------------------- +68: [17:55:01] Test multithreading Locale Switching +152: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +141: [17:55:01] Rep: 0 Mol:31 166: 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 0.008951 seconds +166: Time elapsed 0.004391 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 @@ -30328,30 +29481,76 @@ 166: 5: PASSED. matchedRefRes = 12 166: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 166: 6: PASSED. matchedRefRes = 10 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() 166: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] +141: [17:55:01] Rep: 0 Mol:8 166: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] +68: [17:55:01] Test multithreading (Done) +68: [17:55:01] ------------------------------------- 166: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] -160: ...................... -160: ---------------------------------------------------------------------- -160: Ran 35 tests in 0.548s -160: -160: OK -160: json lasso 166: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 166: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 12: PASSED. matchedRefRes = 8 +159: file rxn_test1_6.png gave hash 3642317125U not the expected 483353696U +106: ....... +106: ---------------------------------------------------------------------- +106: Ran 21 tests in 1.007s +106: +106: OK +106: (Five aromatic carbons And (Not any of Five aromatic carbons)) +106: (Five aromatic carbons Or (Not any of Five aromatic carbons)) +106: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) +106: ******************************************** +106: Testing: PAINS_A 2 +106: ******************************************** +106: Testing: PAINS_B 4 +106: ******************************************** +106: Testing: PAINS_C 8 +106: ******************************************** +106: Testing: PAINS 14 +106: (Not FilterMatcher) +106: Bar +106: Count 1 +106: ******************************************** +106: {'Cl,Br,I'} +106: 1 +106: 2 +106: running 166: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 13: PASSED. matchedRefRes = 9 166: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 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: [17:55:01] Rep: 0 Mol:12 +141: [17:55:01] Rep: 0 Mol:16 +68: *************************************** +68: *************************************** +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +141: [17:55:01] Rep: 0 Mol:21 +68: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [17:55:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +157: processing +157: launch :0 +157: launch :1 +157: launch :2 +127/230 Test #156: pyMolCatalog ........................... Passed 0.38 sec +test 169 + Start 169: testRascalCluster + +169: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +169: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +169: Test timeout computed to be: 1500 +157: launch :3 +141: [17:55:01] Rep: 0 Mol:25 +141: [17:55:01] Rep: 0 Mol:14 +141: [17:55:01] Rep: 0 Mol:20 166: 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] @@ -30361,14 +29560,13 @@ 166: ----------------------------------- 166: 166: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -166: Time elapsed 0.013863 seconds +166: Time elapsed 0.004920 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] 166: 2: PASSED. matchedRefRes = 1 166: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 166: 3: PASSED. matchedRefRes = 6 -146: [09:08:28] Molecule does not have explicit Hs. Consider calling AddHs() 166: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 166: 4: PASSED. matchedRefRes = 13 166: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] @@ -30377,22 +29575,37 @@ 166: 6: PASSED. matchedRefRes = 10 166: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 7: NOREF. Reference data NOT LISTED in test case. +141: [17:55:01] Rep: 0 Mol:29 166: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 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. 166: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 +159: file rxn_test1_7.png gave hash 1818284781U not the expected 528963379U +141: [17:55:01] Rep: 0 Mol:18 166: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 11: NOREF. Reference data NOT LISTED in test case. +68: [17:55:01] bond with order 0 found on line 7. This is not part of the MDL specification. 166: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 12: PASSED. matchedRefRes = 8 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() 166: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 13: PASSED. matchedRefRes = 9 +159: file rxn_test1_7.svg gave hash 3432246161U not the expected 1389845691U +159: Done +159: ----------------- Test 2: some examples that caused problems in testing 166: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 166: 14: PASSED. matchedRefRes = 11 +141: [17:55:01] Rep: 0 Mol:24 166: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 15: PASSED. matchedRefRes = 2 +139: processing +139: launch :0 +139: launch :1 +139: launch :2 +139: [17:55:01] Rep: 0 Mol:1 +139: launch :3 166: 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] @@ -30402,7 +29615,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -166: Time elapsed 0.004821 seconds +166: Time elapsed 0.001210 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] @@ -30417,6 +29630,20 @@ 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 +139: [17:55:01] Rep: 0 Mol:3 +139: [17:55:01] Rep: 0 Mol:0 +139: [17:55:01] Rep: 0 Mol:2 +141: [17:55:01] Rep: 0 Mol:28 +141: [17:55:01] Rep: 0 Mol:22 +128/230 Test #154: pyShapeHelpers ......................... Passed 0.47 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-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +170: Test timeout computed to be: 1500 +139: [17:55:01] Rep: 0 Mol:5 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -30424,9 +29651,11 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.009966 seconds +166: Time elapsed 0.007960 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. +159: file rxn_test2_1.png gave hash 1441990148U not the expected 399415052U +141: [17:55:01] Rep: 0 Mol:26 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] @@ -30441,10 +29670,12 @@ 166: 7: NOREF. Reference data NOT LISTED in test case. 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. +139: [17:55:01] Rep: 0 Mol:9 166: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 166: 10: NOREF. Reference data NOT LISTED in test case. +139: [17:55:01] Rep: 0 Mol:4 166: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] @@ -30459,37 +29690,60 @@ 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. +68: [17:55:01] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [17:55:01] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +139: [17:55:01] Rep: 0 Mol:13 +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. +68: [17:55:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +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 +141: [17:55:01] Rep: 0 Mol:30 166: 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: 166: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -166: Time elapsed 0.014857 seconds +166: Time elapsed 0.006091 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. +139: [17:55:01] Rep: 0 Mol:17 166: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 166: 3: NOREF. Reference data NOT LISTED in test case. 166: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 166: 4: NOREF. Reference data NOT LISTED in test case. +139: [17:55:01] Rep: 0 Mol:6 166: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 166: 5: NOREF. Reference data NOT LISTED in test case. 166: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 166: 6: NOREF. Reference data NOT LISTED in test case. +139: [17:55:01] Rep: 0 Mol:8 166: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 166: 7: NOREF. Reference data NOT LISTED in test case. 166: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 166: 8: NOREF. Reference data NOT LISTED in test case. +139: [17:55:01] Rep: 0 Mol:10 166: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 166: 10: NOREF. Reference data NOT LISTED in test case. +159: file rxn_test2_2_1.png gave hash 1239682505U not the expected 1215378243U +158: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U 166: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 166: 11: NOREF. Reference data NOT LISTED in test case. +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +129/230 Test #143: pyForceFieldHelpers .................... Passed 0.75 sec +test 171 + Start 171: testCIPLabeler + +171: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler +171: Test timeout computed to be: 1500 166: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 166: 12: NOREF. Reference data NOT LISTED in test case. 166: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] @@ -30508,466 +29762,480 @@ 166: --- ALL PASSED --- 166: ----------------------------------- 166: 5 TEST CASES FAILED -147/230 Test #166: testMMPA ............................... Passed 0.36 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-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -167: Test timeout computed to be: 1500 -148/230 Test #160: pyMolDraw2D ............................ Passed 2.11 sec -test 168 - Start 168: testRascalMCES - -168: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -168: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -168: Test timeout computed to be: 1500 -144: validating reference data -165: .... -165: ---------------------------------------------------------------------- -165: Ran 4 tests in 0.019s -165: -165: OK -146: [09:08:29] Molecule does not have explicit Hs. Consider calling AddHs() -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 -149/230 Test #165: pyMolHash .............................. Passed 0.99 sec -test 169 - Start 169: testRascalCluster - -169: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -169: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -169: Test timeout computed to be: 1500 -146: [09:08:29] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:08:30] Molecule does not have explicit Hs. Consider calling AddHs() -161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -161: Time elapsed 0.000 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 0.069 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 0.009 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 0.015 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 0.118 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 0.120 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 0.270 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 0.255 seconds -161: -161: testSegFault() -161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.018 seconds -161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.029 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 0.020 seconds -161: -161: testThreshold() -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: Time elapsed 0.000 seconds -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 0.761 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 0.929 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 0.472 seconds -161: -161: testAtomCompareIsotopes() -161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -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: 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 -161: Time elapsed 0.002 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 0.008 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 0.108 seconds -161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -161: Time elapsed 0.002 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 0.033 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 0.0014 seconds. bond[0]=6 -161: STATISTICS: -161: Total Growing Steps = 1, MCS found on 1 step, for 0.0014 seconds -161: Initial Seeds = 1, Mismatched 0 -161: Inspected Seeds = 2 -161: Rejected by BestSize = 0 -161: IndividualBondExcluded = 0 -161: MatchCheck Seeds = 2 -161: MatchCalls = 2 -161: MatchFound = 1 -161: fastMatchCalls = 1 -161: fastMatchFound = 0 -161: slowMatchCalls = 2 -161: slowMatchFound = 1 -161: DupCacheFound = 0 0 matched, 0 mismatched -161: HashCache size = 1 keys -161: HashCache size = 1 entries -161: FindHashInCache = 2 -161: HashFoundInCache= 0 -161: ExactMatchCalls = 0 -161: ExactMatchFound = 0 -161: Time elapsed 0.002 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 -161: res sub = 1 size=3 -161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CCC(F)Cl query = CC useChirality = 0 -161: res sub = 1 size=2 -161: MCS: [#6]-[#6] 2 atoms, 1 bonds -161: test target = CCC(F)Cl query = CC useChirality = 1 -161: res sub = 1 size=2 -161: MCS: [#6]-[#6] 2 atoms, 1 bonds -161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -161: res sub = 0 size=0 -161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = OC(F)CCl query = OC(F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = OC(F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#9] 1 atoms, 0 bonds -161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#9] 1 atoms, 0 bonds -161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: -161: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: done -158: file testHandDrawn-5a.svg gave hash 1022103754U not the expected 3628607349U -158: [09:08:30] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:30] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-5b.svg gave hash 541506982U not the expected 2522138089U -158: [09:08:30] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [09:08:30] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-5.png gave hash 3431298533U not the expected 3439548169U -158: file testBrackets-5a.svg gave hash 279553678U not the expected 3061667963U -158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -158: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U -158: [09:08:31] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U -158: file testGithub4238_1.png gave hash 1615966361U not the expected 3410617836U -158: file testGithub4323_1.png gave hash 4251183326U not the expected 3723958844U -158: file testGithub4323_3.png gave hash 304742911U not the expected 2185913679U -158: [09:08:31] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -146: .[09:08:31] Molecule does not have explicit Hs. Consider calling AddHs() -161: [09:08:31] The provided InitialSeed is not an MCS and will be ignored -144: processing -144: launch :0 -144: launch :1 -144: launch :2 -144: launch :3 -158: file testFlexiCanvas.2a.png gave hash 4288280796U not the expected 3217758043U -158: file testFlexiCanvas.2b.png gave hash 3583431125U not the expected 4070063910U -158: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -148: processing -148: launch :0 -148: launch :1 -148: launch :2 -148: launch :3 -93: 0,0 0 -93: 0,1 0 -93: 1,0 0 -93: 1,1 0 -93: 2,0 0 -93: 2,1 0 -150/230 Test #93: testEnumeration ........................ Passed 18.69 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-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -170: Test timeout computed to be: 1500 -158: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -158: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -158: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -158: file testGithub4764.sz1.png gave hash 1930422547U not the expected 98827714U -158: file testGithub4764.sz2.png gave hash 2441829654U not the expected 89252465U -158: file testGithub4764.sz3.png gave hash 3374802290U not the expected 148503574U -158: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U -158: file github5383_1.svg gave hash 4241964660U not the expected 3666750661U -158: file github5383_2.svg gave hash 2560846108U not the expected 0U -158: file github5383_1.png gave hash 2818284953U not the expected 992803933U -158: file acs1996_1.png gave hash 342575424U not the expected 2957839025U -158: file acs1996_2.svg gave hash 908745273U not the expected 1521279517U -158: file acs1996_2.png gave hash 496998965U not the expected 2664798808U -158: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -158: file acs1996_5.svg gave hash 3624853279U not the expected 1680320774U -158: file acs1996_8.svg gave hash 4110469272U not the expected 2477908768U -158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U -158: [09:08:33] 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 bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U -158: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -170: ..........Too many matching bond pairs (1032) so can't continue. -158: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U -158: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U -158: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U -158: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U -158: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U -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 -158: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U -123: Warning: Atom Count for residue GLU150A does not match expected count -123: Warning: Atom Count for residue ASN157A does not match expected count -158: file github6504_2.svg gave hash 106020287U not the expected 2871662880U -158: file github6569_1.svg gave hash 1698514747U not the expected 116573839U -158: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U -123: =============================================================================== -123: All tests passed (515 assertions in 10 test cases) -123: -151/230 Test #123: descriptorsTestCatch ................... Passed 17.13 sec -test 171 - Start 171: testCIPLabeler - -171: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler -171: Test timeout computed to be: 1500 -167: ......... -167: ---------------------------------------------------------------------- -167: Ran 9 tests in 5.529s -167: -167: OK -171: Randomness seeded to: 3980464096 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] non kekulizable aromatic bond being treated as bond order 1 -171: [09:08:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -171: [09:08:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -152/230 Test #167: pyMMPA ................................. Passed 6.71 sec +130/230 Test #166: testMMPA ............................... Passed 0.20 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-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 172: Test timeout computed to be: 1500 -171: =============================================================================== -171: All tests passed (6572 assertions in 18 test cases) -171: -153/230 Test #171: testCIPLabeler ......................... Passed 0.43 sec +160: ...[17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +160: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +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 +139: [17:55:01] Rep: 0 Mol:12 +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 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +152: ..[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +139: [17:55:01] Rep: 0 Mol:16 +139: [17:55:01] Rep: 0 Mol:7 +152: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +68: check isomorphism +139: [17:55:01] Rep: 0 Mol:11 +152: .[17:55:01] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +152: [17:55:01] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +152: ... +152: ---------------------------------------------------------------------- +152: Ran 9 tests in 0.164s +152: +152: OK +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +139: [17:55:01] Rep: 0 Mol:15 +139: [17:55:01] Rep: 0 Mol:19 +159: file rxn_test2_2_2.png gave hash 2733977819U not the expected 3645141778U +158: file testHandDrawn-1.png gave hash 3356982379U not the expected 698316547U +139: [17:55:01] Rep: 0 Mol:21 +139: [17:55:01] Rep: 0 Mol:23 +139: [17:55:01] Rep: 0 Mol:27 +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 +171: Randomness seeded to: 1463777662 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +139: [17:55:01] Rep: 0 Mol:20 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +171: [17:55:01] non kekulizable aromatic bond being treated as bond order 1 +139: [17:55:01] Rep: 0 Mol:31 +139: [17:55:01] Rep: 0 Mol:14 +139: [17:55:01] Rep: 0 Mol:25 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +159: file rxn_test2_2_3.png gave hash 3575777004U not the expected 551946805U +139: [17:55:01] Rep: 0 Mol:24 +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 +160: ..........[17:55:01] +160: +160: **** +160: Pre-condition Violation +160: molecule must not be None +160: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +160: Failed Expression: m +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so +160: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so +160: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +160: 5# 0x00007FF67103562C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +160: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +160: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +160: 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-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +160: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +160: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +160: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +160: 12# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +160: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +160: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +160: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 16# 0x00007FF6707AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 17# 0x00007FF6707AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 18# 0x00007FF6707AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 19# 0x00007FF6707AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 20# 0x00007FF6707AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +160: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so +160: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so +160: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so +160: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so +160: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +160: 26# 0x00007FF6710323C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +160: 27# _PyObject_MakeTpCall in /usr/bin/python3 +160: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 29# 0x0000000000546E76 in /usr/bin/python3 +160: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 31# _PyObject_Call_Prepend in /usr/bin/python3 +160: 32# 0x000000000059D6E4 in /usr/bin/python3 +160: 33# _PyObject_MakeTpCall in /usr/bin/python3 +160: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 35# 0x0000000000546E76 in /usr/bin/python3 +160: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 37# _PyObject_Call_Prepend in /usr/bin/python3 +160: 38# 0x000000000059D6E4 in /usr/bin/python3 +160: 39# _PyObject_MakeTpCall in /usr/bin/python3 +160: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 41# 0x0000000000546E76 in /usr/bin/python3 +160: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 43# _PyObject_Call_Prepend in /usr/bin/python3 +160: 44# 0x000000000059D6E4 in /usr/bin/python3 +160: 45# _PyObject_MakeTpCall in /usr/bin/python3 +160: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 47# _PyObject_Call_Prepend in /usr/bin/python3 +160: 48# 0x000000000059810D in /usr/bin/python3 +160: 49# 0x0000000000593E22 in /usr/bin/python3 +160: 50# _PyObject_MakeTpCall in /usr/bin/python3 +160: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +160: 52# PyEval_EvalCode in /usr/bin/python3 +160: 53# 0x00000000005FFE7F in /usr/bin/python3 +160: 54# 0x00000000006A59F2 in /usr/bin/python3 +160: 55# _PyRun_SimpleFileObject in /usr/bin/python3 +160: 56# _PyRun_AnyFileObject in /usr/bin/python3 +160: 57# Py_RunMain in /usr/bin/python3 +160: 58# Py_BytesMain in /usr/bin/python3 +160: 59# 0x00007FF673828D68 in /lib/x86_64-linux-gnu/libc.so.6 +160: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +160: 61# _start in /usr/bin/python3 +160: ---------- +160: **** +160: +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +131/230 Test #106: pyFilterCatalog ........................ Passed 1.48 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-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 173: Test timeout computed to be: 1500 -172: .... -172: ---------------------------------------------------------------------- -172: Ran 4 tests in 0.044s -172: -172: OK -154/230 Test #172: pyCIPLabelsWrapTest .................... Passed 1.13 sec +139: [17:55:01] Rep: 0 Mol:28 +139: [17:55:01] Rep: 0 Mol:29 +139: [17:55:01] Rep: 0 Mol:18 +159: file rxn_test2_2_4.png gave hash 4049234447U not the expected 4234617566U +159: Done +159: ----------------- Test 3: test reactant highlighting +139: [17:55:01] Rep: 0 Mol:22 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +139: [17:55:01] Rep: 0 Mol:26 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +139: [17:55:01] Rep: 0 Mol:30 +159: file rxn_test3_1.png gave hash 3887561208U not the expected 4176857511U +159: Done +159: ----------------- Test 4: some examples from SMARTS in testing +159: draw! +165: .... +165: ---------------------------------------------------------------------- +165: Ran 4 tests in 0.031s +165: +165: OK +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +132/230 Test #152: pyChemicalFeatures ..................... Passed 0.67 sec test 174 Start 174: deprotectTest 174: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 174: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 174: Test timeout computed to be: 1500 -174: Randomness seeded to: 2874380384 -174: =============================================================================== -174: All tests passed (111 assertions in 3 test cases) -174: -155/230 Test #174: deprotectTest .......................... Passed 0.11 sec +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testHandDrawn-2.svg gave hash 1534109833U not the expected 4132716144U +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +159: file rxn_test4_1.png gave hash 1743844008U not the expected 4187207676U +159: done +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testHandDrawn-2.png gave hash 3620124651U not the expected 1605553248U +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +171: [17:55:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +171: [17:55:01] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +158: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +87: [17:55:01] Explicit valence for atom # 9 N, 6, is greater than permitted +158: file testHandDrawn-3.png gave hash 1463224710U not the expected 2881952238U +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +159: file rxn_test4_2.png gave hash 2769144016U not the expected 3490081297U +158: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U +158: [17:55:01] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:01] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +171: =============================================================================== +171: All tests passed (6572 assertions in 18 test cases) +171: +133/230 Test #171: testCIPLabeler ......................... Passed 0.23 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-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 175: Test timeout computed to be: 1500 -158: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U -158: file AtropManyChiralsEnhanced.svg gave hash 3759358369U not the expected 348414093U -158: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U -170: ... -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 3.138s -170: -170: OK -156/230 Test #170: pyRascalMCES ........................... Passed 4.26 sec +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +159: Done +134/230 Test #159: moldraw2DRxnTest1 ...................... Passed 0.66 sec test 176 Start 176: testReducedGraphs 176: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 176: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 176: Test timeout computed to be: 1500 -158: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U -158: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U -158: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U -158: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U -158: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U -158: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U -158: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U -158: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U +158: file testHandDrawn-4.png gave hash 2460067691U not the expected 3431655453U +135/230 Test #165: pyMolHash .............................. Passed 0.57 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-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +177: Test timeout computed to be: 1500 +146: .[17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +115: =>start test AUTOCORR3D custom +115: [17:55:01] test on : 365 molecules done +124: Warning: Atom Count for residue ASN39A does not match expected count 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: +174: Randomness seeded to: 3393206430 +174: =============================================================================== +174: All tests passed (111 assertions in 3 test cases) +174: +136/230 Test #174: deprotectTest .......................... Passed 0.16 sec +test 178 + Start 178: trajectoryTest + +178: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory +178: 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, 0.3, 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, 0.3, 1, 0.3, 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, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 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, 0.3, 1, 0.6, 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, 0.3, 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, ] 176: 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, 0, 0, 0, 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, 0.6, 1, 0.3, 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, 1.3, 1.3, 0.6, 1, 0.6, 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, 0.3, 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, ] 176: +160: ...................... +160: ---------------------------------------------------------------------- +160: Ran 35 tests in 0.320s +160: +160: OK +160: json lasso +139: [17:55:01] Rep: 20 Mol:3 +139: [17:55:01] Rep: 20 Mol:7 +139: [17:55:01] Rep: 20 Mol:11 +139: [17:55:01] Rep: 20 Mol:15 +139: [17:55:01] Rep: 20 Mol:19 176: 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, 0, 0, 0, 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, 0.6, 1, 0.3, 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, 1.3, 1.3, 0.6, 1, 0.6, 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, 0.3, 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, ] 176: +139: [17:55:01] Rep: 20 Mol:0 176: 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: +139: [17:55:01] Rep: 20 Mol:4 +139: [17:55:01] Rep: 20 Mol:23 +139: [17:55:01] Rep: 20 Mol:27 +139: [17:55:01] Rep: 20 Mol:31 +139: [17:55:01] Rep: 20 Mol:8 +139: [17:55:01] Rep: 20 Mol:12 +139: [17:55:01] Rep: 20 Mol:16 176: 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0.3, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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: -157/230 Test #176: testReducedGraphs ...................... Passed 0.05 sec -test 177 - Start 177: pyReducedGraphs +139: [17:55:01] Rep: 20 Mol:20 +139: [17:55:01] Rep: 20 Mol:24 +139: [17:55:01] Rep: 20 Mol:28 +137/230 Test #176: testReducedGraphs ...................... Passed 0.08 sec +test 179 + Start 179: substructLibraryTest -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-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -177: Test timeout computed to be: 1500 +179: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +179: Test timeout computed to be: 1500 +139: [17:55:01] Rep: 20 Mol:1 +139: [17:55:01] Rep: 20 Mol:5 +139: [17:55:01] Rep: 20 Mol:9 +139: [17:55:01] Rep: 20 Mol:13 +139: [17:55:01] Rep: 20 Mol:17 +139: [17:55:01] Rep: 20 Mol:21 +139: [17:55:01] Rep: 20 Mol:25 +139: [17:55:01] Rep: 20 Mol:29 +138/230 Test #160: pyMolDraw2D ............................ Passed 0.80 sec +test 180 + Start 180: substructLibraryCatchTest + +180: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +180: Test timeout computed to be: 1500 +179: [17:55:01] ------------------------------------- +179: [17:55:01] Test1 +146: [17:55:01] Molecule does not have explicit Hs. Consider calling AddHs() +87: [17:55:01] Explicit valence for atom # 3 Al, 6, is greater than permitted +124: Warning: Atom Count for residue GLU53A does not match expected count +139: [17:55:01] Rep: 20 Mol:2 +139: [17:55:01] Rep: 20 Mol:6 +139: [17:55:01] Rep: 20 Mol:10 +139: [17:55:01] Rep: 20 Mol:14 +139: [17:55:01] Rep: 20 Mol:18 +139: [17:55:01] Rep: 20 Mol:22 +139: [17:55:01] Rep: 20 Mol:26 +139: [17:55:01] Rep: 20 Mol:30 +139: [17:55:02] Rep: 40 Mol:3 +87: [17:55:02] Explicit valence for atom # 4 Al, 6, is greater than permitted +141: [17:55:02] Rep: 100 Mol:3 +141: [17:55:02] Rep: 100 Mol:7 +141: [17:55:02] Rep: 100 Mol:11 +141: [17:55:02] Rep: 100 Mol:15 +141: [17:55:02] Rep: 100 Mol:19 +141: [17:55:02] Rep: 100 Mol:23 +141: [17:55:02] Rep: 100 Mol:27 +139: [17:55:02] Rep: 40 Mol:7 +139: [17:55:02] Rep: 40 Mol:11 +139: [17:55:02] Rep: 40 Mol:15 +139: [17:55:02] Rep: 40 Mol:19 +139: [17:55:02] Rep: 40 Mol:23 +139: [17:55:02] Rep: 40 Mol:27 +139: [17:55:02] Rep: 40 Mol:31 +141: [17:55:02] Rep: 100 Mol:31 +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +87: [17:55:02] Explicit valence for atom # 10 Si, 6, is greater than permitted +115: =>start test 2 WHIM custom +115: [17:55:02] test on : 365 molecules done +146: [17:55:02] Molecule does not have explicit Hs. Consider calling AddHs() +124: Warning: Atom Count for residue ARG64A does not match expected count +139: [17:55:02] Rep: 40 Mol:0 +139: [17:55:02] Rep: 40 Mol:4 +139: [17:55:02] Rep: 40 Mol:8 +139: [17:55:02] Rep: 40 Mol:12 +139: [17:55:02] Rep: 40 Mol:16 +139: [17:55:02] Rep: 40 Mol:20 +139: [17:55:02] Rep: 40 Mol:24 +139: [17:55:02] Rep: 40 Mol:1 +139: [17:55:02] Rep: 40 Mol:5 +139: [17:55:02] Rep: 40 Mol:9 +139: [17:55:02] Rep: 40 Mol:13 +139: [17:55:02] Rep: 40 Mol:17 +139: [17:55:02] Rep: 40 Mol:28 +139: [17:55:02] Rep: 40 Mol:21 +139: [17:55:02] Rep: 40 Mol:25 +139: [17:55:02] Rep: 40 Mol:29 +177: ..... +177: ---------------------------------------------------------------------- +177: Ran 5 tests in 0.049s +177: +177: OK +172: .... +172: ---------------------------------------------------------------------- +172: Ran 4 tests in 0.039s +172: +172: OK +123: Warning: Atom Count for residue GLU150A does not match expected count +141: [17:55:02] Rep: 100 Mol:1 +141: [17:55:02] Rep: 100 Mol:5 +141: [17:55:02] Rep: 100 Mol:9 +141: [17:55:02] Rep: 100 Mol:13 +141: [17:55:02] Rep: 100 Mol:17 +141: [17:55:02] Rep: 100 Mol:21 +141: [17:55:02] Rep: 100 Mol:25 +141: [17:55:02] Rep: 100 Mol:29 +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +179: [17:55:02] done +27: All 191 tests passed +124: Warning: Atom Count for residue LYS80A does not match expected count +179: [17:55:02] ------------------------------------- +179: [17:55:02] Test2 +141: [17:55:02] Rep: 100 Mol:0 +141: [17:55:02] Rep: 100 Mol:4 +141: [17:55:02] Rep: 100 Mol:8 +141: [17:55:02] Rep: 100 Mol:12 +139/230 Test #178: trajectoryTest ......................... Passed 0.51 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-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +181: Test timeout computed to be: 1500 +141: [17:55:02] Rep: 100 Mol:16 +141: [17:55:02] Rep: 100 Mol:20 +141: [17:55:02] Rep: 100 Mol:24 +141: [17:55:02] Rep: 100 Mol:28 +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +170: ..........Too many matching bond pairs (1032) so can't continue. +123: Warning: Atom Count for residue ASN157A does not match expected count +140/230 Test #177: pyReducedGraphs ........................ Passed 0.60 sec +test 182 + Start 182: testRGroupDecomp + +182: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +182: Test timeout computed to be: 1500 +146: [17:55:02] Molecule does not have explicit Hs. Consider calling AddHs() +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +115: =>start test 1 WHIM custom +115: [17:55:02] test on : 365 molecules done +141/230 Test #172: pyCIPLabelsWrapTest .................... Passed 0.86 sec +test 183 + Start 183: testRGroupDecompInternals + +183: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +183: Test timeout computed to be: 1500 +87: [17:55:02] Explicit valence for atom # 2 O, 4, is greater than permitted +139: [17:55:02] Rep: 60 Mol:3 +139: [17:55:02] Rep: 60 Mol:7 +139: [17:55:02] Rep: 60 Mol:11 +139: [17:55:02] Rep: 60 Mol:15 +139: [17:55:02] Rep: 60 Mol:19 +139: [17:55:02] Rep: 60 Mol:23 +139: [17:55:02] Rep: 60 Mol:27 +139: [17:55:02] Rep: 60 Mol:31 +87: [17:55:02] Explicit valence for atom # 3 Be, 4, is greater than permitted +87: [17:55:02] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [17:55:02] Explicit valence for atom # 27 P, 6, is greater than permitted +139: [17:55:02] Rep: 40 Mol:2 +139: [17:55:02] Rep: 40 Mol:6 +139: [17:55:02] Rep: 40 Mol:10 +141: [17:55:02] Rep: 100 Mol:2 +141: [17:55:02] Rep: 100 Mol:6 +141: [17:55:02] Rep: 100 Mol:10 +141: [17:55:02] Rep: 100 Mol:14 +141: [17:55:02] Rep: 100 Mol:18 +141: [17:55:02] Rep: 100 Mol:22 +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +139: [17:55:02] Rep: 40 Mol:14 +139: [17:55:02] Rep: 40 Mol:18 +141: [17:55:02] Rep: 100 Mol:26 +139: [17:55:02] Rep: 40 Mol:22 +141: [17:55:02] Rep: 100 Mol:30 +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +139: [17:55:02] Rep: 40 Mol:26 +139: [17:55:02] Rep: 40 Mol:30 +145: [17:55:02] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +87: =============================================================================== +87: All tests passed (21162 assertions in 3 test cases) +87: +142/230 Test #87: multithreadedSupplierCatchTest ......... Passed 2.50 sec +test 184 + Start 184: rgroupCatchTests + +184: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +184: Test timeout computed to be: 1500 175: ..... 175: ---------------------------------------------------------------------- -175: Ran 5 tests in 0.116s +175: Ran 5 tests in 0.094s 175: 175: OK 175: Testing tert-butyldimethylsilyl @@ -31020,500 +30288,134 @@ 175: Testing acetamide 175: Testing carbobenzyloxy 175: Testing Acetal/Ketal -158: file testGithub_7739_1.svg gave hash 1477601334U not the expected 52079325U -158/230 Test #175: pyDeprotect ............................ Passed 0.79 sec -test 178 - Start 178: trajectoryTest - -178: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory -178: Test timeout computed to be: 1500 -124: Warning: Atom Count for residue GLU5A does not match expected count -124: Warning: Atom Count for residue ASN39A does not match expected count -124: Warning: Atom Count for residue GLU53A does not match expected count -124: Warning: Atom Count for residue ARG64A does not match expected count -124: Warning: Atom Count for residue LYS80A does not match expected count -124: Warning: Atom Count for residue GLU150A does not match expected count -124: Warning: Atom Count for residue ASN157A does not match expected count -124: .[09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: .[09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: ..[09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: .[09:08:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ...[09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -124: [09:08:37] DEPRECATION WARNING: please use MorganGenerator -158: file testGithub_7739_3.svg gave hash 4066656179U not the expected 1126644226U -124: ....[09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:37] DEPRECATION WARNING: please use AtomPairGenerator -124: ....[09:08:38] DEPRECATION WARNING: please use AtomPairGenerator -124: [09:08:38] DEPRECATION WARNING: please use AtomPairGenerator -124: .[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ..[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: .[09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [09:08:38] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ... -124: ---------------------------------------------------------------------- -124: Ran 31 tests in 19.155s -124: -124: OK -124: exactmw 78.046950192 -124: amw 78.11399999999999 -124: lipinskiHBA 0.0 -124: lipinskiHBD 0.0 -124: NumRotatableBonds 0.0 -124: NumHBD 0.0 -124: NumHBA 0.0 -124: NumHeavyAtoms 6.0 -124: NumAtoms 6.0 -124: NumHeteroatoms 0.0 -124: NumAmideBonds 0.0 -124: FractionCSP3 0.0 -124: NumRings 1.0 -124: NumAromaticRings 1.0 -124: NumAliphaticRings 0.0 -124: NumSaturatedRings 0.0 -124: NumHeterocycles 0.0 -124: NumAromaticHeterocycles 0.0 -124: NumSaturatedHeterocycles 0.0 -124: NumAliphaticHeterocycles 0.0 -124: NumSpiroAtoms 0.0 -124: NumBridgeheadAtoms 0.0 -124: NumAtomStereoCenters 0.0 -124: NumUnspecifiedAtomStereoCenters 0.0 -124: labuteASA 37.43140311949697 -124: tpsa 0.0 -124: CrippenClogP 1.6866 -124: CrippenMR 26.441999999999993 -124: chi0v 3.464101615137755 -124: chi1v 2.0000000000000004 -124: chi2v 0.6666666666666671 -124: chi3v 0.6666666666666671 -124: chi4v 0.38490017945975075 -124: chi0n 3.464101615137755 -124: chi1n 2.0000000000000004 -124: chi2n 0.6666666666666671 -124: chi3n 0.6666666666666671 -124: chi4n 0.38490017945975075 -124: hallKierAlpha -0.78 -124: kappa1 3.4115708812260532 -124: kappa2 1.6057694396735218 -124: kappa3 0.5823992601400448 -124: Phi 0.9130327103921437 -124: exactmw 78.046950192 -124: lipinskiHBA 0.0 -158: file testGithub_7739_4.svg gave hash 1029970961U not the expected 9844878U -158: [09:08:38] -158: -158: **** -158: Pre-condition Violation -158: -158: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -158: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x000055B20506F715 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: [09:08:38] -158: -158: **** -158: Range Error -158: idx -158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -158: Failed Expression: 2 < 0 -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x000055B20506EE82 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: [09:08:38] -158: -158: **** -158: Range Error -158: idx -158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -158: Failed Expression: 0 < 0 -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x000055B20506F7E8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x000055B205148548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x000055B205149068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x000055B2051494E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x000055B20511B203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x000055B20511B56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x000055B20506824E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x00007F4A8BC31D68 in /lib/x86_64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -158: 17# 0x000055B205068291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: =============================================================================== -158: All tests passed (6801 assertions in 105 test cases) -158: -159/230 Test #158: moldraw2DTestCatch ..................... Passed 11.49 sec -test 179 - Start 179: substructLibraryTest - -179: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -179: Test timeout computed to be: 1500 -160/230 Test #124: pyMolDescriptors ....................... Passed 19.90 sec -test 180 - Start 180: substructLibraryCatchTest - -180: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -180: Test timeout computed to be: 1500 -179: [09:08:38] ------------------------------------- -179: [09:08:38] Test1 -177: ..... -177: ---------------------------------------------------------------------- -177: Ran 5 tests in 0.023s -177: -177: OK -161/230 Test #177: pyReducedGraphs ........................ Passed 0.82 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-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -181: Test timeout computed to be: 1500 -169: Randomness seeded to: 1676980870 -169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -179: [09:08:38] done -179: [09:08:38] ------------------------------------- -179: [09:08:38] Test2 -162: ........................................[09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: .[09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: [09:08:38] The provided InitialSeed is not an MCS and will be ignored -162: ................. -162: ---------------------------------------------------------------------- -162: Ran 60 tests in 11.213s -162: -162: OK -162/230 Test #162: pyFMCS ................................. Passed 11.77 sec -test 182 - Start 182: testRGroupDecomp - -182: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -182: Test timeout computed to be: 1500 -179: [09:08:39] done -179: [09:08:39] ------------------------------------- -179: [09:08:39] Test3 (stereo options) -163/230 Test #178: trajectoryTest ......................... Passed 1.26 sec -test 183 - Start 183: testRGroupDecompInternals - -183: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -183: Test timeout computed to be: 1500 -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -164/230 Test #183: testRGroupDecompInternals .............. Passed 0.10 sec -test 184 - Start 184: rgroupCatchTests - -184: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -184: Test timeout computed to be: 1500 -179: [09:08:39] Done (stereo options) -179: [09:08:39] ------------------------------------- -179: [09:08:39] Test4 (trusted smiles) -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -179: [09:08:39] Done (trusted smiles) -179: [09:08:39] ------------------------------------- -179: [09:08:39] Testing C++ docs -179: [09:08:39] Done (C++ doc tests) -179: [09:08:39] ------------------------------------- -179: [09:08:39] Testing C++ ring query: PatternHolder -179: [09:08:39] Done (C++ ring query tests) -179: [09:08:39] ------------------------------------- -179: [09:08:39] Testing C++ ring query: TautomerPatternHolder -179: [09:08:39] Done (C++ ring query tests) -179: [09:08:39] ------------------------------------- -179: [09:08:39] Add Patterns -27: All 191 tests passed -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -182: [09:08:39] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -182: [09:08:39] WARNING: not removing hydrogen atom with dummy atom neighbors -184: Randomness seeded to: 2922787517 -184: =============================================================================== -184: All tests passed (1475 assertions in 14 test cases) -184: -165/230 Test #184: rgroupCatchTests ....................... Passed 0.55 sec +143/230 Test #183: testRGroupDecompInternals .............. Passed 0.14 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-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 185: Test timeout computed to be: 1500 -180: Randomness seeded to: 310564961 +139: [17:55:02] Rep: 60 Mol:0 +139: [17:55:02] Rep: 60 Mol:4 +139: [17:55:02] Rep: 60 Mol:8 +139: [17:55:02] Rep: 60 Mol:12 +139: [17:55:02] Rep: 60 Mol:1 +139: [17:55:02] Rep: 60 Mol:5 +139: [17:55:02] Rep: 60 Mol:9 +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +139: [17:55:02] Rep: 60 Mol:13 +139: [17:55:02] Rep: 60 Mol:16 +139: [17:55:02] Rep: 60 Mol:20 +139: [17:55:02] Rep: 60 Mol:17 +139: [17:55:02] Rep: 60 Mol:21 +139: [17:55:02] Rep: 60 Mol:25 +139: [17:55:02] Rep: 60 Mol:24 +139: [17:55:02] Rep: 60 Mol:28 +139: [17:55:02] Rep: 60 Mol:29 +96: . +96: ---------------------------------------------------------------------- +96: Ran 11 tests in 2.196s +96: +96: OK +96: True +96: == CartesianProductStrategy CartesianProductStrategy +96: 197 out of 300 +96: 0 6 out of 10 +96: 1 3 out of 5 +96: 2 4 out of 6 +96: 198 out of 300 +96: 0 10 out of 10 +96: 1 5 out of 5 +96: 2 6 out of 6 +96: Skipped 10000000 in 0.07626175880432129 seconds +96: Skipped 10000000 in 0.9985299110412598 seconds +96: Skipped 10000000 in 0.7860255241394043 seconds +180: Randomness seeded to: 2659042564 180: =============================================================================== 180: All tests passed (171 assertions in 5 test cases) 180: -166/230 Test #180: substructLibraryCatchTest .............. Passed 1.71 sec +144/230 Test #180: substructLibraryCatchTest .............. Passed 0.68 sec test 186 Start 186: molInterchangeTest1 186: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 186: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 186: Test timeout computed to be: 1500 -186: [09:08:39] test1: basics -186: [09:08:39] done -186: [09:08:39] 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: [09:08:39] done -186: [09:08:39] 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: [09:08:39] done -186: [09:08:39] 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: [09:08:39] done -186: [09:08:39] 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: [09:08:39] testing parse options -186: [09:08:39] done -186: [09:08:39] 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: [09:08:39] done -186: [09:08:39] testing 'either' stereochemistry -186: [09:08:39] done -167/230 Test #186: molInterchangeTest1 .................... Passed 0.12 sec +120: =>start test GETAWAY +120: [17:55:02] test on : 365 molecules done +145/230 Test #120: testGETAWAY ............................ Passed 2.27 sec test 187 Start 187: molInterchangeCatchTest 187: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 187: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 187: Test timeout computed to be: 1500 -157: Done -157: ----------------- Test Github #781: Rendering single-atom molecules -157: Done -157: ----------------- Test 3 -187: Randomness seeded to: 3737209786 -187: [09:08:40] unrecognized bond type 12 set to zero while writing -187: [09:08:40] unrecognized bond type 0 set to zero while writing -157: file test3_1.png gave hash 1514877476U not the expected 3984824963U +186: [17:55:02] test1: basics +187: Randomness seeded to: 2126245345 +187: [17:55:02] unrecognized bond type 12 set to zero while writing +187: [17:55:02] unrecognized bond type 0 set to zero while writing 187: =============================================================================== 187: All tests passed (122 assertions in 6 test cases) 187: -168/230 Test #187: molInterchangeCatchTest ................ Passed 0.12 sec +146/230 Test #187: molInterchangeCatchTest ................ Passed 0.04 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-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 188: Test timeout computed to be: 1500 -157: file test3_2.png gave hash 895995063U not the expected 238321316U -157: file test3_3.png gave hash 2806558077U not the expected 414888185U -157: file test3_4.png gave hash 3204576434U not the expected 2265825690U -157: file test3_5.png gave hash 3784843232U not the expected 1911551403U -168: Randomness seeded to: 1143299777 -168: Timed out after 11 seconds. -157: file test3_6.png gave hash 2648864811U not the expected 577293879U -157: file test3_7.png gave hash 727952731U not the expected 248355372U -157: Done -157: ----------------- Test Github774: upside-down drawings -157: file test774_1.png gave hash 1746502640U not the expected 927423591U -157: file test774_2.png gave hash 1057482804U not the expected 1171827286U -157: Done -157: ----------------- Test 9 (molecule legends) -157: file test9_1.svg gave hash 923579170U not the expected 1484349178U -157: Done -157: ----------------- Test Github852: Lines used to wedge bonds are too thick -157: file test852_1.png gave hash 3083219870U not the expected 736085072U -157: file test852_2.png gave hash 1999141294U not the expected 1438089260U -157: ---------------- -157: ---------------- -157: ---------------- -157: ---------------- -157: Done -157: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -157: file test860_1.png gave hash 667708706U not the expected 2065140854U -157: file test860_2.png gave hash 2350165565U not the expected 3098360765U -157: file test860_3.png gave hash 3798998670U not the expected 3439618110U -157: Done -157: ----------------- Test Github #910: ugly coordinates generated for peptide chains -157: Done -157: ----------------- Test Github #932: mistake in SVG for wedged bonds -157: Done -157: ----------------- Test Github #953: default color should not be cyan -157: Done -157: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly -157: Done -157: ----------------- Test Deuterium, Tritium -157: Done -157: ----------------- Test crossed bonds -157: Done -157: ----------------- Testing drawing a second molecule -157: Done -157: ----------------- Testing drawing a grid of molecules -157: Done -157: ----------------- Testing drawMolecules -157: file test12_1.svg gave hash 2982175789U not the expected 881731720U -157: Done -157: ----------------- Test JSON Configuration -157: Done -157: ----------------- Testing github 1090: escape html characters in SVG output -157: Done -157: ----------------- Testing github 1035: overflow bug in SVG color generation -157: Done -157: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes -157: Done -157: ----------------- Testing github 1322: add custom atom labels -157: Done -157: ----------------- Testing use of a black & white palette -157: Done -157: ----------------- Testing use of continuous highlighting with drawMolecules -157: Done -157: ----------------- Test 17 - Testing maximum font size -188: .. -188: ---------------------------------------------------------------------- -188: Ran 2 tests in 0.039s -188: -188: OK -157: Done -157: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list -157: Done -157: ----------------- Testing use of fixed scales for drawing. -157: Done -157: ----------------- Testing rotation of 2D drawing. -157: Done -157: ----------------- Testing inclusion of molecule metadata -157: Done -157: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default -157: Done -157: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions -157: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U -157: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U -157: Done -157: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn -157: Done -157: ----------------- Testing testGithub2931: multi-coloured molecule highlights. -157: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U -157: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U -157: Done -157: ----------------- Testing annotation of 2D Drawing. -157: file test20_1.png gave hash 2978996523U not the expected 1672353490U -169/230 Test #188: pyMolInterchange ....................... Passed 1.42 sec +186: [17:55:02] done +186: [17:55:02] 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: [17:55:02] done +186: [17:55:02] 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: [17:55:02] done +186: [17:55:02] 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: [17:55:02] done +186: [17:55:02] 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: [17:55:02] testing parse options +186: [17:55:02] done +186: [17:55:02] 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: [17:55:02] done +186: [17:55:02] testing 'either' stereochemistry +186: [17:55:02] done +147/230 Test #186: molInterchangeTest1 .................... Passed 0.07 sec test 189 Start 189: testSLNParse 189: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 189: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 189: Test timeout computed to be: 1500 -157: file test20_2.png gave hash 745058850U not the expected 1073213605U +148/230 Test #175: pyDeprotect ............................ Passed 0.92 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-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap +190: Test timeout computed to be: 1500 +139: [17:55:02] Rep: 80 Mol:3 +149/230 Test #96: pyChemReactionEnumerations ............. Passed 2.65 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-x86_64-linux-gnu/Code/GraphMol/Wrap +191: Test timeout computed to be: 1500 +139: [17:55:02] Rep: 80 Mol:7 +139: [17:55:02] Rep: 80 Mol:11 +139: [17:55:02] Rep: 80 Mol:15 +139: [17:55:02] Rep: 80 Mol:19 +139: [17:55:02] Rep: 80 Mol:23 +139: [17:55:02] Rep: 80 Mol:27 +139: [17:55:02] Rep: 80 Mol:31 189: 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: @@ -31527,131 +30429,385 @@ 189: 2 0->3 order: 1 189: 3 0->4 order: 1 189: 4 0->5 order: 1 -189: [09:08:41] SLN Parse Error: syntax error while parsing: CH4[I=13] -189: [09:08:41] Failed parsing SLN 'CH4[I=13]' -189: [09:08:41] SLN Parser error: Atom ID 1 appears *after* its ring closure. -189: [09:08:41] SLN Parser error: Ring closure 1 does not have a corresponding opener. -189: [09:08:41] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -189: [09:08:41] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -189: [09:08:41] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -189: [09:08:41] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -189: [09:08:41] SLN Parse Error: syntax error while parsing: CH4 fff -189: [09:08:41] Failed parsing SLN 'CH4 fff' -189: [09:08:41] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -189: [09:08:41] Failed parsing SLN 'C[charge=+1] foo' -189: [09:08:41] Query property 'is' ignored on non-query atom -189: [09:08:41] Query property 'is' ignored on non-query atom -170/230 Test #189: testSLNParse ........................... Passed 0.07 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-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap -190: Test timeout computed to be: 1500 -157: file test20_3.png gave hash 472521001U not the expected 471234756U -157: file test20_4.png gave hash 1015859242U not the expected 2803490234U -157: Done -157: ----------------- Test 21 - different font -157: Done -157: ----------------- Test 22 - draw explicit methyls. -157: Done -157: ----------------- Testing drawing of legends. -157: Done -157: ----------------- Test Github 3305 - change and scale line widths. -157: file testGithub3305_1.png gave hash 588173490U not the expected 1801411420U -157: file testGithub3305_2.png gave hash 3393765154U not the expected 2904846519U -157: file testGithub3305_3.png gave hash 694090236U not the expected 2915229647U -157: file testGithub3305_4.png gave hash 3784843232U not the expected 1911551403U -157: file testGithub3305_5.png gave hash 2382054754U not the expected 614319597U -157: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U -157: file testGithub3305_6.png gave hash 1247498295U not the expected 3926947401U -157: file testGithub3305_7.png gave hash 3628125988U not the expected 1720405002U -157: Done -157: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. -157: Done -157: ----------------- Test Github 4156 - bad scale for radicals in grid -157: Done -157: ----------------- Test JSON atomColourPalette -157: Done -157: ----------------- Test draw aromatic OR queries -157: Done -157: ----------------- Test AND queries -157: Done -171/230 Test #157: moldraw2DTest1 ......................... Passed 16.02 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-x86_64-linux-gnu/Code/GraphMol/Wrap -191: Test timeout computed to be: 1500 -190: .. -190: ---------------------------------------------------------------------- -190: Ran 2 tests in 0.027s -190: -190: OK -172/230 Test #190: pySLNParse ............................. Passed 0.91 sec +189: [17:55:02] SLN Parse Error: syntax error while parsing: CH4[I=13] +189: [17:55:02] Failed parsing SLN 'CH4[I=13]' +189: [17:55:02] SLN Parser error: Atom ID 1 appears *after* its ring closure. +189: [17:55:02] SLN Parser error: Ring closure 1 does not have a corresponding opener. +189: [17:55:02] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +189: [17:55:02] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +189: [17:55:02] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +189: [17:55:02] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +189: [17:55:02] SLN Parse Error: syntax error while parsing: CH4 fff +189: [17:55:02] Failed parsing SLN 'CH4 fff' +189: [17:55:02] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +189: [17:55:02] Failed parsing SLN 'C[charge=+1] foo' +189: [17:55:02] Query property 'is' ignored on non-query atom +189: [17:55:02] Query property 'is' ignored on non-query atom +150/230 Test #189: testSLNParse ........................... Passed 0.07 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-x86_64-linux-gnu/Code/GraphMol/Wrap 192: Test timeout computed to be: 1500 -79: =============================================================================== -79: All tests passed (1586 assertions in 98 test cases) -79: -173/230 Test #79: fileParsersCatchTest ................... Passed 29.23 sec +146: [17:55:02] Molecule does not have explicit Hs. Consider calling AddHs() +179: [17:55:02] done +139: [17:55:02] Rep: 80 Mol:0 +139: [17:55:02] Rep: 80 Mol:4 +139: [17:55:02] Rep: 80 Mol:8 +139: [17:55:02] Rep: 80 Mol:12 +139: [17:55:02] Rep: 80 Mol:16 +179: [17:55:02] ------------------------------------- +179: [17:55:02] Test3 (stereo options) +139: [17:55:02] Rep: 80 Mol:20 +139: [17:55:02] Rep: 80 Mol:24 +139: [17:55:02] Rep: 80 Mol:28 +139: [17:55:02] Rep: 60 Mol:2 +139: [17:55:02] Rep: 60 Mol:6 +139: [17:55:02] Rep: 60 Mol:10 +139: [17:55:02] Rep: 60 Mol:14 +139: [17:55:02] Rep: 60 Mol:18 +139: [17:55:02] Rep: 60 Mol:22 +139: [17:55:02] Rep: 60 Mol:26 +139: [17:55:02] Rep: 80 Mol:1 +139: [17:55:02] Rep: 80 Mol:5 +139: [17:55:02] Rep: 80 Mol:9 +139: [17:55:02] Rep: 60 Mol:30 +139: [17:55:02] Rep: 80 Mol:13 +139: [17:55:02] Rep: 80 Mol:17 +39: [17:55:02] done: 500000 +39: [17:55:02] Done +139: [17:55:02] Rep: 80 Mol:21 +139: [17:55:02] Rep: 80 Mol:25 +139: [17:55:02] Rep: 80 Mol:29 +179: [17:55:02] Done (stereo options) +179: [17:55:02] ------------------------------------- +179: [17:55:02] Test4 (trusted smiles) +39: [17:55:02] Testing hanoi with a functor. +39: [17:55:02] Done +39: [17:55:02] Testing basic partition refinement. +39: [17:55:02] Done +39: [17:55:02] Testing partition refinement with neighbors. +39: [17:55:02] Done +39: [17:55:02] testing canonicalization via tie breaking. +39: [17:55:02] Done +39: [17:55:02] testing canonicalization using the wrapper. +146: [17:55:02] Molecule does not have explicit Hs. Consider calling AddHs() +39: [17:55:02] Done +39: [17:55:02] testing some specific ordering problems +39: [17:55:02] Finished +39: [17:55:02] testing chiral invariants. +39: [17:55:02] Finished +39: [17:55:02] testing unique ranks in w.r.t. renumbering. +184: Randomness seeded to: 683539810 +184: =============================================================================== +184: All tests passed (1475 assertions in 14 test cases) +184: +151/230 Test #184: rgroupCatchTests ....................... Passed 0.47 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-x86_64-linux-gnu/Code/GraphMol/Wrap 193: Test timeout computed to be: 1500 -191: ..............[09:08:43] SMARTS Parse Error: syntax error while parsing: fiib -191: [09:08:43] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -191: ....[09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] Spurious data before the first property will be ignored -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] Spurious data before the first property will be ignored -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] Property will be truncated after the first blank line -191: [09:08:43] ERROR: Problems encountered parsing data fields -191: [09:08:43] ERROR: moving to the beginning of the next molecule -191: [09:08:43] Property will be truncated after the first blank line -191: .[09:08:43] SMILES Parse Error: syntax error while parsing: fail -191: [09:08:43] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -191: [09:08:43] ERROR: Smiles parse error on line 2 -191: [09:08:43] ERROR: Cannot create molecule from : 'fail' -191: >>> This may result in an infinite loop. It should finish almost instantly -191: <<< OK, it finished. -191: ............[09:08:43] Explicit valence for atom # 1 C, 5, is greater than permitted -191: ......[09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [09:08:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +179: [17:55:02] Done (trusted smiles) +179: [17:55:02] ------------------------------------- +179: [17:55:02] Testing C++ docs +179: [17:55:02] Done (C++ doc tests) +179: [17:55:02] ------------------------------------- +179: [17:55:02] Testing C++ ring query: PatternHolder +179: [17:55:02] Done (C++ ring query tests) +179: [17:55:02] ------------------------------------- +179: [17:55:02] Testing C++ ring query: TautomerPatternHolder +179: [17:55:02] Done (C++ ring query tests) +179: [17:55:02] ------------------------------------- +179: [17:55:02] Add Patterns +182: [17:55:02] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +182: [17:55:02] WARNING: not removing hydrogen atom with dummy atom neighbors +39: [17:55:03] Finished +39: [17:55:03] testing mol fragments. +39: [17:55:03] Finished +39: [17:55:03] testing protein round-tripping. +124: Warning: Atom Count for residue GLU150A does not match expected count +188: .. +188: ---------------------------------------------------------------------- +188: Ran 2 tests in 0.021s +188: +188: OK +124: Warning: Atom Count for residue ASN157A does not match expected count +139: [17:55:03] Rep: 80 Mol:2 +139: [17:55:03] Rep: 80 Mol:6 +139: [17:55:03] Rep: 80 Mol:10 +139: [17:55:03] Rep: 80 Mol:14 +139: [17:55:03] Rep: 80 Mol:18 +139: [17:55:03] Rep: 80 Mol:22 +139: [17:55:03] Rep: 80 Mol:26 +139: [17:55:03] Rep: 80 Mol:30 +190: .. +190: ---------------------------------------------------------------------- +190: Ran 2 tests in 0.011s +190: +190: OK +158: file testHandDrawn-5a.svg gave hash 1022103754U not the expected 3628607349U +158: [17:55:03] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:03] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 192: ...... 192: ---------------------------------------------------------------------- -192: Ran 6 tests in 0.073s +192: Ran 6 tests in 0.017s 192: 192: OK -191: ........[09:08:43] non-ring atom 0 marked aromatic -191: [09:08:43] non-ring atom 0 marked aromatic -191: [09:08:43] +68: [17:55:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [17:55:03] 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: [17:55:03] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0x00007F043E8C7CB1 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0x00007F043E8D161A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# 0x00007F043E8D199D in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 6# 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-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 9# 0x000056043CA0CCF5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x000056043CA734F2 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0x000056043C9F39E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 12# 0x00007F043DE33D68 in /lib/x86_64-linux-gnu/libc.so.6 +68: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +68: 14# 0x000056043C9F3B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +158: file testHandDrawn-5b.svg gave hash 541506982U not the expected 2522138089U +158: [17:55:03] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [17:55:03] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +152/230 Test #192: pyTestConformerWrap .................... Passed 0.55 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-x86_64-linux-gnu/Code/GraphMol/Wrap +194: Test timeout computed to be: 1500 +153/230 Test #188: pyMolInterchange ....................... Passed 0.65 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-x86_64-linux-gnu/Code/GraphMol/Wrap +195: Test timeout computed to be: 1500 +154/230 Test #190: pySLNParse ............................. Passed 0.63 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-x86_64-linux-gnu/Code/GraphMol/Wrap +196: Test timeout computed to be: 1500 +191: ..............[17:55:03] SMARTS Parse Error: syntax error while parsing: fiib +191: [17:55:03] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +191: ....[17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +191: [17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +191: [17:55:03] Spurious data before the first property will be ignored +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] Property will be truncated after the first blank line +139: [17:55:03] done +139: [17:55:03] ------------------------------------- +139: [17:55:03] Test MMFF multithreading2 +191: [17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +141: [17:55:03] done +141: [17:55:03] ------------------------------------- +141: [17:55:03] Test UFF multithreading2 +191: [17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +191: [17:55:03] Spurious data before the first property will be ignored +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +191: [17:55:03] Property will be truncated after the first blank line +191: [17:55:03] ERROR: Problems encountered parsing data fields +191: [17:55:03] ERROR: moving to the beginning of the next molecule +191: [17:55:03] Property will be truncated after the first blank line +193: [17:55:03] +193: +193: **** +191: .[17:55:03] SMILES Parse Error: syntax error while parsing: fail +191: [17:55:03] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +191: [17:55:03] ERROR: Smiles parse error on line 2 +191: [17:55:03] ERROR: Cannot create molecule from : 'fail' +191: >>> This may result in an infinite loop. It should finish almost instantly +191: <<< OK, it finished. +193: Pre-condition Violation +193: from must be < size() +193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +193: Failed Expression: from < static_cast(size()) +193: ---------- +193: Stacktrace: +193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 +193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so +193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# _PyObject_MakeTpCall in /usr/bin/python3 +193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 24# 0x0000000000546E76 in /usr/bin/python3 +193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 26# _PyObject_Call_Prepend in /usr/bin/python3 +193: 27# 0x000000000059D6E4 in /usr/bin/python3 +193: 28# _PyObject_MakeTpCall in /usr/bin/python3 +193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 30# 0x0000000000546E76 in /usr/bin/python3 +193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 32# _PyObject_Call_Prepend in /usr/bin/python3 +193: 33# 0x000000000059D6E4 in /usr/bin/python3 +193: 34# _PyObject_MakeTpCall in /usr/bin/python3 +193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 36# 0x0000000000546E76 in /usr/bin/python3 +193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 38# _PyObject_Call_Prepend in /usr/bin/python3 +193: 39# 0x000000000059D6E4 in /usr/bin/python3 +193: 40# _PyObject_MakeTpCall in /usr/bin/python3 +193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 42# _PyObject_Call_Prepend in /usr/bin/python3 +193: 43# 0x000000000059810D in /usr/bin/python3 +193: 44# 0x0000000000593E22 in /usr/bin/python3 +193: 45# _PyObject_MakeTpCall in /usr/bin/python3 +193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 47# PyEval_EvalCode in /usr/bin/python3 +193: 48# 0x00000000005FFE7F in /usr/bin/python3 +193: 49# 0x00000000006A59F2 in /usr/bin/python3 +193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 +193: 51# _PyRun_AnyFileObject in /usr/bin/python3 +193: 52# Py_RunMain in /usr/bin/python3 +193: 53# Py_BytesMain in /usr/bin/python3 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +193: 56# _start in /usr/bin/python3 +193: ---------- +193: **** +193: +193: .[17:55:03] +193: +193: **** +158: file testHandDrawn-5.png gave hash 3431298533U not the expected 3439548169U +149: 2280717866 +193: Pre-condition Violation +193: from must be < size() +193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +193: Failed Expression: from < static_cast(size()) +193: ---------- +193: Stacktrace: +193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 +193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so +193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so +193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# _PyObject_MakeTpCall in /usr/bin/python3 +193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 24# 0x0000000000546E76 in /usr/bin/python3 +193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 26# _PyObject_Call_Prepend in /usr/bin/python3 +193: 27# 0x000000000059D6E4 in /usr/bin/python3 +193: 28# _PyObject_MakeTpCall in /usr/bin/python3 +193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 30# 0x0000000000546E76 in /usr/bin/python3 +193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 32# _PyObject_Call_Prepend in /usr/bin/python3 +193: 33# 0x000000000059D6E4 in /usr/bin/python3 +193: 34# _PyObject_MakeTpCall in /usr/bin/python3 +193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 36# 0x0000000000546E76 in /usr/bin/python3 +193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 38# _PyObject_Call_Prepend in /usr/bin/python3 +193: 39# 0x000000000059D6E4 in /usr/bin/python3 +193: 40# _PyObject_MakeTpCall in /usr/bin/python3 +193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 42# _PyObject_Call_Prepend in /usr/bin/python3 +193: 43# 0x000000000059810D in /usr/bin/python3 +193: 44# 0x0000000000593E22 in /usr/bin/python3 +193: 45# _PyObject_MakeTpCall in /usr/bin/python3 +193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +193: 47# PyEval_EvalCode in /usr/bin/python3 +193: 48# 0x00000000005FFE7F in /usr/bin/python3 +193: 49# 0x00000000006A59F2 in /usr/bin/python3 +193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 +193: 51# _PyRun_AnyFileObject in /usr/bin/python3 +193: 52# Py_RunMain in /usr/bin/python3 +193: 53# Py_BytesMain in /usr/bin/python3 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +193: 56# _start in /usr/bin/python3 +193: ---------- +193: **** +193: +191: ............[17:55:03] Explicit valence for atom # 1 C, 5, is greater than permitted +158: file testBrackets-5a.svg gave hash 279553678U not the expected 3061667963U +191: ......[17:55:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [17:55:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [17:55:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [17:55:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +191: ........[17:55:03] non-ring atom 0 marked aromatic +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Issue252: Bad definitions for Crippen atom types. +191: [17:55:03] non-ring atom 0 marked aromatic +191: [17:55:03] 191: 191: **** +158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of ChiVs. 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp @@ -31662,9 +30818,9 @@ 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 4# 0x00007F21EB47C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 4# 0x00007FC5ED07C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -31675,17 +30831,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -31718,15 +30874,15 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [09:08:43] non-ring atom 0 marked aromatic -191: [09:08:43] non-ring atom 0 marked aromatic -191: [09:08:43] +191: [17:55:03] non-ring atom 0 marked aromatic +191: [17:55:03] non-ring atom 0 marked aromatic +191: [17:55:03] 191: 191: **** 191: Range Error @@ -31739,9 +30895,9 @@ 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 4# 0x00007F21EB47C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 4# 0x00007FC5ED07C4C0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -31752,17 +30908,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -31795,162 +30951,270 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ...............[09:08:43] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -191: [09:08:43] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -174/230 Test #192: pyTestConformerWrap .................... Passed 1.26 sec -test 194 - Start 194: pyTestSGroups +158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +191: ...............[17:55:03] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +191: [17:55:03] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of ChiNs. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of HallKierAlpha. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of Kappa1. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of Kappa2. +158: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of Kappa3. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Crippen atom type calculations. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test ring descriptors +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test other count descriptors. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test MQN +191: ..............[17:55:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +191: [17:55:03] Explicit valence for atom # 1 C, 5, is greater than permitted +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test GitHub Issue 56. +109: [17:55:03] WARNING: not removing hydrogen atom without neighbors +109: [17:55:03] WARNING: not removing hydrogen atom without neighbors +109: [17:55:03] WARNING: not removing hydrogen atom without neighbors +109: [17:55:03] WARNING: not removing hydrogen atom without neighbors +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github92: Bad Crippen atom type for pyrrole H. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github362: order dependence in Kier-Hall descriptors. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test calculation of spiro and bridgehead counts. +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github694: ExactMolWt ignoring the mass of the electron +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Testing Properties and KitchenSink +144: [17:55:00] --------------------------------- +144: [17:55:00] test3 +144: +144: [17:55:00] --------------------------------- +144: [17:55:00] test4 +144: +144: [17:55:00] --------------------------------- +144: [17:55:00] test5 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test6 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test15Dists +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test Issue 215 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testMultipleConfs +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testMultipleConfsExpTors +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue227 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue236 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testOrdering +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue244 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue251 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue276 +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue284 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue285 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testIssue355 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] testRandomCoords +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 1989539 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 2091864 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test constrained embedding +144: +144: [17:55:03] ssd: 0.0752641 +109: [17:55:03] ---Caught keyerror (bad property name)--- +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test USR Descriptor +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github #1973: support P and S terms for TPSA calculation +109: [17:55:03] done +109: [17:55:03] ------------------------------------- +109: [17:55:03] Test Github #2948: Empty molecule has non-zero LabuteASA +109: [17:55:03] done +144: [17:55:03] ssd: 0.0659363 +155/230 Test #109: testDescriptors ........................ Passed 3.53 sec +test 197 + Start 197: pyTestPropertyLists -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-x86_64-linux-gnu/Code/GraphMol/Wrap -194: Test timeout computed to be: 1500 -193: [09:08:43] -193: -193: **** -193: Pre-condition Violation -193: from must be < size() -193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -193: Failed Expression: from < static_cast(size()) -193: ---------- -193: Stacktrace: -193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 -193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so -193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# _PyObject_MakeTpCall in /usr/bin/python3 -193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 24# 0x0000000000546E76 in /usr/bin/python3 -193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 26# _PyObject_Call_Prepend in /usr/bin/python3 -193: 27# 0x000000000059D6E4 in /usr/bin/python3 -193: 28# _PyObject_MakeTpCall in /usr/bin/python3 -193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 30# 0x0000000000546E76 in /usr/bin/python3 -193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 32# _PyObject_Call_Prepend in /usr/bin/python3 -193: 33# 0x000000000059D6E4 in /usr/bin/python3 -193: 34# _PyObject_MakeTpCall in /usr/bin/python3 -193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 36# 0x0000000000546E76 in /usr/bin/python3 -193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 38# _PyObject_Call_Prepend in /usr/bin/python3 -193: 39# 0x000000000059D6E4 in /usr/bin/python3 -193: 40# _PyObject_MakeTpCall in /usr/bin/python3 -193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 42# _PyObject_Call_Prepend in /usr/bin/python3 -193: 43# 0x000000000059810D in /usr/bin/python3 -193: 44# 0x0000000000593E22 in /usr/bin/python3 -193: 45# _PyObject_MakeTpCall in /usr/bin/python3 -193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 47# PyEval_EvalCode in /usr/bin/python3 -193: 48# 0x00000000005FFE7F in /usr/bin/python3 -193: 49# 0x00000000006A59F2 in /usr/bin/python3 -193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 -193: 51# _PyRun_AnyFileObject in /usr/bin/python3 -193: 52# Py_RunMain in /usr/bin/python3 -193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 -193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -193: 56# _start in /usr/bin/python3 -193: ---------- -193: **** -193: -193: .[09:08:43] -193: -193: **** -193: Pre-condition Violation -193: from must be < size() -193: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -193: Failed Expression: from < static_cast(size()) -193: ---------- -193: Stacktrace: -193: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -193: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 -193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so -193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so -193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# _PyObject_MakeTpCall in /usr/bin/python3 -193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 24# 0x0000000000546E76 in /usr/bin/python3 -193: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 26# _PyObject_Call_Prepend in /usr/bin/python3 -193: 27# 0x000000000059D6E4 in /usr/bin/python3 -193: 28# _PyObject_MakeTpCall in /usr/bin/python3 -193: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 30# 0x0000000000546E76 in /usr/bin/python3 -193: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 32# _PyObject_Call_Prepend in /usr/bin/python3 -193: 33# 0x000000000059D6E4 in /usr/bin/python3 -193: 34# _PyObject_MakeTpCall in /usr/bin/python3 -193: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 36# 0x0000000000546E76 in /usr/bin/python3 -193: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 38# _PyObject_Call_Prepend in /usr/bin/python3 -193: 39# 0x000000000059D6E4 in /usr/bin/python3 -193: 40# _PyObject_MakeTpCall in /usr/bin/python3 -193: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 42# _PyObject_Call_Prepend in /usr/bin/python3 -193: 43# 0x000000000059810D in /usr/bin/python3 -193: 44# 0x0000000000593E22 in /usr/bin/python3 -193: 45# _PyObject_MakeTpCall in /usr/bin/python3 -193: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -193: 47# PyEval_EvalCode in /usr/bin/python3 -193: 48# 0x00000000005FFE7F in /usr/bin/python3 -193: 49# 0x00000000006A59F2 in /usr/bin/python3 -193: 50# _PyRun_SimpleFileObject in /usr/bin/python3 -193: 51# _PyRun_AnyFileObject in /usr/bin/python3 -193: 52# Py_RunMain in /usr/bin/python3 -193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 -193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -193: 56# _start in /usr/bin/python3 -193: ---------- -193: **** -193: -191: ..............[09:08:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -191: [09:08:43] Explicit valence for atom # 1 C, 5, is greater than permitted -193: .[09:08:44] +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-x86_64-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 +158: [17:55:03] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U +68: [17:55:03] 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: [17:55:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +146: [17:55:03] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testGithub4238_1.png gave hash 1615966361U not the expected 3410617836U +139: [17:55:03] done +139: [17:55:03] ------------------------------------- +139: [17:55:03] Test MMFF multithreading3 +158: file testGithub4323_1.png gave hash 4251183326U not the expected 3723958844U +141: [17:55:03] done +141: [17:55:03] ------------------------------------- +141: [17:55:03] Test UFF multithreading3 +146: [17:55:03] Molecule does not have explicit Hs. Consider calling AddHs() +68: ---------------------------------- +68: ---------------------------------- +68: [17:55:03] +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-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +68: 3# 0x000056043CA1A0FF in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x000056043CA7356A in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x000056043C9F39E3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0x00007F043DE33D68 in /lib/x86_64-linux-gnu/libc.so.6 +68: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +68: 8# 0x000056043C9F3B11 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +68: [17:55:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +196: .s. +196: ---------------------------------------------------------------------- +196: Ran 3 tests in 0.194s +196: +196: OK (skipped=1) +196: Testing Smiles and SD MultithreadedMolSupplier +170: ... +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 2.108s +170: +170: OK +158: file testGithub4323_3.png gave hash 304742911U not the expected 2185913679U +167: ......... +167: ---------------------------------------------------------------------- +167: Ran 9 tests in 2.256s +167: +167: OK +39: [17:55:03] Finished +39: [17:55:03] testing stability w.r.t. renumbering. +158: [17:55:03] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +139: [17:55:04] done +139: [17:55:04] ------------------------------------- +139: [17:55:04] Testing github 162: Incorrect SMILES after MMFF parameterization . +139: [17:55:04] done +139: [17:55:04] ------------------------------------- +139: [17:55:04] Testing github 224: crash during MMFF parameterization . +139: [17:55:04] done +139: [17:55:04] ------------------------------------- +139: [17:55:04] Testing github6728: crash due to missing stretch-bend params. +156/230 Test #170: pyRascalMCES ........................... Passed 2.59 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-x86_64-linux-gnu/Code/GraphMol/Wrap +198: Test timeout computed to be: 1500 +194: ............. +194: ---------------------------------------------------------------------- +194: Ran 13 tests in 0.054s +194: +194: OK +194: Testing SubstanceGroups wrapper +157/230 Test #139: testMMFFForceFieldHelpers .............. Passed 3.38 sec +test 199 + Start 199: molStandardizeTest + +199: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +199: Test timeout computed to be: 1500 +158/230 Test #167: pyMMPA ................................. Passed 2.74 sec +test 200 + Start 200: molNormalizeTest + +200: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +200: Test timeout computed to be: 1500 +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 2091974 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 2835784 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 3019283 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 3238580 +144: +144: [17:55:03] --------------------------------- +144: [17:55:03] test sf.net issue 3483968 +144: +144: [17:55:04] --------------------------------- +144: [17:55:04] test github issue 55 +144: +144: [17:55:04] --------------------------------- +144: [17:55:04] test1 +144: +144: [17:55:04] --------------------------------- +144: [17:55:04] test multi-threading +144: +144: building molecules +193: .[17:55:04] 193: 193: **** 193: Range Error @@ -31965,23 +31229,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 @@ -32014,13 +31278,15 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 55# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[09:08:44] +39: [17:55:04] Finished +39: [17:55:04] testing smiles round-tripping. +193: .[17:55:04] 193: 193: **** 193: Pre-condition Violation @@ -32034,23 +31300,23 @@ 193: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32083,13 +31349,14 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: ..[09:08:44] +144: generating reference data +193: ..[17:55:04] 193: 193: **** 193: Pre-condition Violation @@ -32103,23 +31370,23 @@ 193: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32152,13 +31419,14 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[09:08:44] +200: [17:55:04] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +193: .[17:55:04] 193: 193: **** 193: Pre-condition Violation @@ -32172,23 +31440,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32221,13 +31489,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [09:08:44] +193: [17:55:04] 193: 193: **** 193: Pre-condition Violation @@ -32241,23 +31509,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32290,13 +31558,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[09:08:44] +193: .[17:55:04] 193: 193: **** 193: Range Error @@ -32311,23 +31579,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 @@ -32360,15 +31628,26 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 55# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [09:08:44] +193: [17:55:04] 193: 193: **** +159/230 Test #194: pyTestSGroups .......................... Passed 0.87 sec +test 201 + Start 201: molValidateTest + +201: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +201: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +201: Test timeout computed to be: 1500 +149: 724325920 +149: =============================================================================== +149: All tests passed (73 assertions in 3 test cases) +149: 193: Range Error 193: pointNum 193: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -32380,23 +31659,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32429,13 +31708,20 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[09:08:44] +160/230 Test #149: molAlignCatchTest ...................... Passed 3.25 sec +test 202 + Start 202: molChargeTest + +202: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +202: Test timeout computed to be: 1500 +193: .[17:55:04] 193: 193: **** 193: Range Error @@ -32450,23 +31736,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x0000000000546E76 in /usr/bin/python3 @@ -32499,15 +31785,23 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 55# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [09:08:44] +193: [17:55:04] 193: 193: **** +161/230 Test #196: pyTestMultithreadedMolSupplier ......... Passed 0.86 sec +146: [17:55:04] Molecule does not have explicit Hs. Consider calling AddHs() +test 203 + Start 203: molTautomerTest + +203: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +203: Test timeout computed to be: 1500 193: Pre-condition Violation 193: d_dimension must be == 2 193: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -32519,23 +31813,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32568,13 +31862,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [09:08:44] +193: [17:55:04] 193: 193: **** 193: Pre-condition Violation @@ -32588,23 +31882,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x00007F2404CE362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x00007F43C63DC62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x00007F24023AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x00007F24023AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x00007F24023AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x00007F24023AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x00007F24023AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x00007F43C39AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x00007F43C39AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x00007F43C39AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x00007F43C39AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x00007F43C39AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 17# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 18# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 19# 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-x86_64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x00007F2404CE03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x00007F43C63D93C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x0000000000546E76 in /usr/bin/python3 @@ -32637,7 +31931,7 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x00007F2405499D68 in /lib/x86_64-linux-gnu/libc.so.6 +193: 54# 0x00007F43C6B84D68 in /lib/x86_64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- @@ -32645,33 +31939,39 @@ 193: 193: . 193: ---------------------------------------------------------------------- -193: Ran 9 tests in 0.637s +193: Ran 9 tests in 0.827s 193: 193: OK 193: Testing Trajectory wrapper -185: .................... -185: ---------------------------------------------------------------------- -185: Ran 20 tests in 4.025s -185: -185: OK -175/230 Test #193: pyTestTrajectory ....................... Passed 1.29 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-x86_64-linux-gnu/Code/GraphMol/Wrap -195: Test timeout computed to be: 1500 -191: ............................[09:08:44] unable to set wavy bonds for double bonds: 3 -176/230 Test #185: pyRGroupDecomposition .................. Passed 5.14 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-x86_64-linux-gnu/Code/GraphMol/Wrap -196: Test timeout computed to be: 1500 -191: .............[09:08:45] +141: [17:55:04] done +141: [17:55:04] ------------------------------------- +141: [17:55:04] Testing GitHubIssue62. +191: ............................[17:55:04] unable to set wavy bonds for double bonds: 3 +141: [17:55:04] beta-lactam 39.6387 +141: [17:55:04] cyclopropanone 174.698 +141: [17:55:04] aziridine 337.986 +141: [17:55:04] aziridinone 115.248 +141: [17:55:04] isobutene 2.48217 +141: [17:55:04] acetone 1.91788 +141: [17:55:04] cyclopentanone 10.1648 +141: [17:55:04] cyclopropene 99.4921 +141: [17:55:04] cyclobutene 41.0156 +191: .............[17:55:04] 191: 191: **** +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 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp @@ -32684,7 +31984,7 @@ 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32695,17 +31995,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -32738,584 +32038,152 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- -191: **** -191: -194: ............. -194: ---------------------------------------------------------------------- -194: Ran 13 tests in 0.138s -194: -194: OK -194: Testing SubstanceGroups wrapper -50: Randomness seeded to: 860647536 -50: =============================================================================== -50: All tests passed (14835 assertions in 14 test cases) -50: -177/230 Test #50: canonTestsCatch ........................ Passed 31.97 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-x86_64-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 -178/230 Test #194: pyTestSGroups .......................... Passed 1.73 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-x86_64-linux-gnu/Code/GraphMol/Wrap -198: Test timeout computed to be: 1500 -196: .s. -196: ---------------------------------------------------------------------- -196: Ran 3 tests in 0.442s -196: -196: OK (skipped=1) -196: Testing Smiles and SD MultithreadedMolSupplier -197: [09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: .[09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: ...[09:08:46] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [09:08:46] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [09:08:46] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: . -197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.017s -197: -197: OK -179/230 Test #197: pyTestPropertyLists .................... Passed 0.97 sec -test 199 - Start 199: molStandardizeTest - -199: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -199: Test timeout computed to be: 1500 -180/230 Test #196: pyTestMultithreadedMolSupplier ......... Passed 1.46 sec -test 200 - Start 200: molNormalizeTest - -200: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -200: Test timeout computed to be: 1500 -198: . -198: ---------------------------------------------------------------------- -198: Ran 1 test in 0.033s -198: -198: OK -200: [09:08:46] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -182: iterative -179: [09:08:46] ------------------------------------- -179: [09:08:46] testing PatternHolder -181/230 Test #198: pyCDXMLTest ............................ Passed 1.37 sec -test 201 - Start 201: molValidateTest - -201: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -201: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -201: Test timeout computed to be: 1500 -200: [09:08:46] Initializing Normalizer -200: [09:08:46] Running Normalizer -200: [09:08:46] Rule applied: BrokenazidetoN=N+=N- -200: [09:08:46] Initializing Normalizer -200: [09:08:46] Running Normalizer -200: [09:08:46] Initializing Normalizer -200: [09:08:46] Running Normalizer -182/230 Test #200: molNormalizeTest ....................... Passed 0.62 sec -test 202 - Start 202: molChargeTest - -202: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -202: Test timeout computed to be: 1500 -150: .............[09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -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 +141: [17:55:04] cyclopropane 267.236 201: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -183/230 Test #202: molChargeTest .......................... Passed 0.13 sec -test 203 - Start 203: molTautomerTest - -203: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -203: Test timeout computed to be: 1500 -179: [09:08:47] ------------------------------------- -179: [09:08:47] testing TautomerPatternHolder -184/230 Test #201: molValidateTest ........................ Passed 0.24 sec +191: **** +191: +141: [17:55:04] gamma-lactam 15.7471 +162/230 Test #193: pyTestTrajectory ....................... Passed 1.27 sec test 204 Start 204: molStandardizeSmallTest 204: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 204: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 -185/230 Test #204: molStandardizeSmallTest ................ Passed 0.08 sec +200: [17:55:04] Initializing Normalizer +200: [17:55:04] Running Normalizer +200: [17:55:04] Rule applied: BrokenazidetoN=N+=N- +200: [17:55:04] Initializing Normalizer +200: [17:55:04] Running Normalizer +163/230 Test #201: molValidateTest ........................ Passed 0.11 sec test 205 Start 205: molFragmentTest 205: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 205: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -191: ....................[09:08:47] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:47] Explicit valence for atom # 6 F, 2, is greater than permitted -191: [09:08:47] Can't kekulize mol. Unkekulized atoms: 3 4 5 -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -205: [09:08:47] SMARTS Parse Error: syntax error while parsing: [Cl -205: [09:08:47] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -186/230 Test #205: molFragmentTest ........................ Passed 0.09 sec +200: [17:55:04] Initializing Normalizer +200: [17:55:04] Running Normalizer +164/230 Test #200: molNormalizeTest ....................... Passed 0.18 sec +165/230 Test #202: molChargeTest .......................... Passed 0.11 sec test 206 Start 206: molStandardizeCatchTest 206: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 206: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -179: [09:08:47] ------------------------------------- -179: [09:08:47] testSegFaultInHolder -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:08:47] dsafsdfSMILES Parse Error: syntax error while parsing: '[09:08:47] -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: dsafsdf -179: while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: while parsing: dsafsdf[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:08:47] dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] [09:08:47] [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: while parsing: dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: ' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: -179: [09:08:47] [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: [09:08:47] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [09:08:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [09:08:47] ------------------------------------- -179: [09:08:47] Results do not depend on numThreads -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:47] Molecule does not have explicit Hs. Consider calling AddHs() -191: .................[09:08:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -187/230 Test #199: molStandardizeTest ..................... Passed 2.04 sec test 207 Start 207: molStandardizePipelineTest 207: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -207: Randomness seeded to: 1316290529 +39: [17:55:04] Finished +39: [17:55:04] testing github #1567: Non-canonical result from MolFragmentToSmiles() +39: [17:55:04] Finished +166/230 Test #39: hanoiTest .............................. Passed 4.46 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-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +208: Test timeout computed to be: 1500 +146: [17:55:04] Molecule does not have explicit Hs. Consider calling AddHs() +207: Randomness seeded to: 1716443628 207: 1 Counts line too short: '' on line4 207: 1 Could not instantiate a valid molecule from input +141: [17:55:04] trans-2,3-diphenylcyclopropan-1-one 203.398 +167/230 Test #204: molStandardizeSmallTest ................ Passed 0.06 sec +test 209 + Start 209: testScaffoldNetwork + +209: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +209: Test timeout computed to be: 1500 207: 8 Molecule has no atoms -207: [09:08:48] Explicit valence for atom # 1 N, 4, is greater than permitted -207: [09:08:48] Explicit valence for atom # 1 N, 4, is greater than permitted +207: [17:55:04] Explicit valence for atom # 1 N, 4, is greater than permitted +207: [17:55:04] 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. +161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +161: Time elapsed 0.000 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 0.092 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 0.012 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 0.019 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 0.164 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 0.137 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 0.152 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 0.164 seconds +161: +161: testSegFault() +161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +161: Time elapsed 0.019 seconds +161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +161: Time elapsed 0.025 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 0.026 seconds +161: +161: testThreshold() +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: Time elapsed 0.000 seconds +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 0.661 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 0.666 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 0.954 seconds +161: +161: testAtomCompareIsotopes() +161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +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 0.010 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 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 @@ -33328,24 +32196,49 @@ 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: [09:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: [17:55:04] 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 +68: [17:55:04] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [17:55:04] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +141: [17:55:04] cis-2,3-diphenylcyclopropan-1-one 206.852 207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 207: 64 Atom 0 has adjacent stereo bonds with like orientation -207: [09:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: [17:55:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [17:55:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [17:55:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [17:55:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +197: .[17:55:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [17:55:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [17:55:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 207: 16 The molecule includes non-null Z coordinates 207: 64 Atom 0 has adjacent stereo bonds with like orientation -206: Randomness seeded to: 1025550055 -206: * - * - * - * m1 +197: ...[17:55:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [17:55:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [17:55:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +197: . +197: ---------------------------------------------------------------------- +197: Ran 5 tests in 0.014s +197: +197: OK +205: [17:55:04] SMARTS Parse Error: syntax error while parsing: [Cl +205: [17:55:04] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' 207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +168/230 Test #205: molFragmentTest ........................ Passed 0.12 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +210: Test timeout computed to be: 1500 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. -206: * - * - * - * m2 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. +141: [17:55:04] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +141: [17:55:04] cyclopropylidencyclobutane 218.879 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 16777216 The representation of some functional groups was adjusted. @@ -33353,17 +32246,51 @@ 207: 67108864 The protonation state was adjusted. 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. -206: * - * - * - * m1 -206: * - * - * - * m2 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. -182: bulk +169/230 Test #197: pyTestPropertyLists .................... Passed 0.73 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +211: Test timeout computed to be: 1500 +68: [17:55:04] Empty atom list: 'M ALS 1 0 F' on line 8. 207: 16777216 The representation of some functional groups was adjusted. 207: 67108864 The protonation state was adjusted. 207: 8388608 One or more metal atoms were disconnected. 207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +141: [17:55:04] diphenylmethylidencyclobutane 79.6139 +141: [17:55:04] done +141: [17:55:04] ------------------------------------- +141: [17:55:04] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +141: [17:55:04] done +141: [17:55:04] ------------------------------------- +141: [17:55:04] Test square planar complexes +141: [17:55:04] done +141: [17:55:04] ------------------------------------- +141: [17:55:04] Test octahedral complexes +141: [17:55:04] done +198: . +198: ---------------------------------------------------------------------- +198: Ran 1 test in 0.013s +198: +198: OK +170/230 Test #68: fileParsersTest1 ....................... Passed 4.49 sec +test 212 + Start 212: testMolEnumerator + +212: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +212: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator +212: Test timeout computed to be: 1500 207: 67108864 The protonation state was adjusted. -206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 3 7 +171/230 Test #141: testUFFForceFieldHelpers ............... Passed 3.70 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-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap +213: Test timeout computed to be: 1500 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. @@ -33373,52 +32300,1708 @@ 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. -206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 3 8 207: 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. 207: 16777216 The "wavy" style of bond 4 was removed -206: [09:08:48] Can't kekulize mol. Unkekulized atoms: 2 3 4 207: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 2 was removed 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 1 was removed +172/230 Test #41: resMolSupplierTest ..................... Passed 4.62 sec +test 214 + Start 214: testAbbreviations + +214: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations +214: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations +214: Test timeout computed to be: 1500 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 1 was removed 207: 16777216 The "wavy" style of bond 4 was removed +161: Time elapsed 0.002 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 0.008 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 0.102 seconds +161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +161: Time elapsed 0.001 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 0.030 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 0.0017 seconds. bond[0]=6 +161: STATISTICS: +161: Total Growing Steps = 1, MCS found on 1 step, for 0.0017 seconds +161: Initial Seeds = 1, Mismatched 0 +161: Inspected Seeds = 2 +161: Rejected by BestSize = 0 +161: IndividualBondExcluded = 0 +161: MatchCheck Seeds = 2 +161: MatchCalls = 2 +161: MatchFound = 1 +161: fastMatchCalls = 1 +161: fastMatchFound = 0 +161: slowMatchCalls = 2 +161: slowMatchFound = 1 +161: DupCacheFound = 0 0 matched, 0 mismatched +161: HashCache size = 1 keys +161: HashCache size = 1 entries +161: FindHashInCache = 2 +161: HashFoundInCache= 0 +161: ExactMatchCalls = 0 +161: ExactMatchFound = 0 +161: Time elapsed 0.002 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 +161: res sub = 1 size=3 207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 207: 16777216 The "wavy" style of bond 3 was removed +161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CCC(F)Cl query = CC useChirality = 0 +161: res sub = 1 size=2 +161: MCS: [#6]-[#6] 2 atoms, 1 bonds +161: test target = CCC(F)Cl query = CC useChirality = 1 +161: res sub = 1 size=2 +161: MCS: [#6]-[#6] 2 atoms, 1 bonds +161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +161: res sub = 0 size=0 +161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = OC(F)CCl query = OC(F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = OC(F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#9] 1 atoms, 0 bonds +161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#9] 1 atoms, 0 bonds +161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: +161: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: done +212: Randomness seeded to: 2509492228 +212: [17:55:04] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +146: [17:55:04] Molecule does not have explicit Hs. Consider calling AddHs() +214: Randomness seeded to: 375094343 +214: [17:55:04] SMARTS Parse Error: syntax error while parsing: *fail +214: [17:55:04] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 207: 16777216 The representation of some functional groups was adjusted. -207: [09:08:48] Can't kekulize mol. Unkekulized atoms: 2 3 5 +173/230 Test #198: pyCDXMLTest ............................ Passed 0.44 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-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap +215: Test timeout computed to be: 1500 +214: [17:55:04] no suitable SubstanceGroups found +214: =============================================================================== +214: All tests passed (195 assertions in 12 test cases) +214: +174/230 Test #214: testAbbreviations ...................... Passed 0.05 sec +test 216 + Start 216: generalizedSubstructCatch + +216: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +216: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +216: Test timeout computed to be: 1500 +207: [17:55:04] Can't kekulize mol. Unkekulized atoms: 2 3 5 +212: =============================================================================== +212: All tests passed (321 assertions in 16 test cases) +212: 207: =============================================================================== 207: All tests passed (268 assertions in 5 test cases) 207: -188/230 Test #207: molStandardizePipelineTest ............. Passed 0.29 sec -test 208 - Start 208: pyMolStandardize +175/230 Test #212: testMolEnumerator ...................... Passed 0.10 sec +test 217 + Start 217: pyGeneralizedSubstruct -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-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -208: Test timeout computed to be: 1500 -203: [09:08:48] Tautomer enumeration stopped at 292 tautomers: max transforms reached -203: [09:08:49] Tautomer enumeration stopped at 292 tautomers: max transforms reached -208: .....[09:08:49] Tautomer enumeration stopped at 292 tautomers: max transforms reached -203: [09:08:49] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -208: [09:08:49] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -208: .[09:08:50] Tautomer enumeration stopped at 25 tautomers: canceled +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-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +217: Test timeout computed to be: 1500 +176/230 Test #207: molStandardizePipelineTest ............. Passed 0.26 sec +test 218 + Start 218: testMolProcessing + +218: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing +218: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing +218: Test timeout computed to be: 1500 +158: file testFlexiCanvas.2a.png gave hash 4288280796U not the expected 3217758043U +158: file testFlexiCanvas.2b.png gave hash 3583431125U not the expected 4070063910U +158: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +146: [17:55:04] Molecule does not have explicit Hs. Consider calling AddHs() +211: . +211: ---------------------------------------------------------------------- +211: Ran 1 test in 0.015s +211: +211: OK +177/230 Test #211: pyScaffoldNetworkPickling .............. Passed 0.35 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-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap +219: Test timeout computed to be: 1500 +158: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +210: ....... +210: ---------------------------------------------------------------------- +210: Ran 7 tests in 0.056s +210: +210: OK +158: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +158: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +158: file testGithub4764.sz1.png gave hash 1930422547U not the expected 98827714U +206: Randomness seeded to: 1144508734 +206: * - * - * - * m1 +216: Randomness seeded to: 1389060216 +216: =============================================================================== +216: All tests passed (486 assertions in 10 test cases) +216: +178/230 Test #216: generalizedSubstructCatch .............. Passed 0.32 sec +test 220 + Start 220: testQuery + +220: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query/testQuery +220: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query +220: Test timeout computed to be: 1500 +206: * - * - * - * m2 +158: file testGithub4764.sz2.png gave hash 2441829654U not the expected 89252465U +220: Query +220: Query2 +220: Equality +220: Greater +220: GreaterEqual +220: Less +220: LessEqual +220: Open Range +220: Closed Range +220: Float +220: With Tolerance +220: Set +220: And +220: Or +220: XOr +220: pointer and copy foo +220: Set2 +179/230 Test #220: testQuery .............................. Passed 0.01 sec +test 221 + Start 221: testMatCalc + +221: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +221: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc +221: Test timeout computed to be: 1500 +206: * - * - * - * m1 +206: * - * - * - * m2 +221: 1.68022e+08 +221: 1.73149e+08 +221: 1.05549e+08 +221: 7.20603e+07 +221: 1.41535e+08 +221: 1.08592e+08 +221: 1.11334e+08 +221: 2.05553e+08 +221: 1.54962e+08 +221: 8.08231e+07 +221: 5.61421e+07 +221: 1.28874e+08 +221: 1.59011e+08 +221: 8.69902e+07 +221: 1.31367e+08 +221: 2.27389e+08 +221: 1.60289e+08 +221: 7.79813e+07 +221: 1.61001e+08 +221: 2.07599e+08 +221: 2.24432e+08 +221: 1.39725e+08 +221: 2.42614e+08 +221: 1.77578e+08 +221: 1.05908e+08 +221: 9.06742e+07 +221: 1.8087e+08 +221: 1.98182e+08 +221: 2.03052e+08 +221: 1.7673e+08 +221: 9.32798e+07 +221: 1.37969e+08 +221: 1.83778e+08 +221: 2.1228e+08 +221: 5.06157e+07 +221: 1.566e+08 +221: 2.37142e+08 +221: 1.49345e+08 +221: 7.05819e+07 +221: 1.71633e+08 +221: 1.96817e+08 +221: 2.18246e+08 +221: 9.49496e+07 +221: 2.25618e+08 +221: 1.30219e+08 +180/230 Test #221: testMatCalc ............................ Passed 0.01 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-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +222: Test timeout computed to be: 1500 +206: [17:55:04] Can't kekulize mol. Unkekulized atoms: 3 7 +206: [17:55:04] Can't kekulize mol. Unkekulized atoms: 3 8 +206: [17:55:04] Can't kekulize mol. Unkekulized atoms: 2 3 4 +215: ....... +215: ---------------------------------------------------------------------- +215: Ran 7 tests in 0.024s +215: +215: OK +181/230 Test #210: pyScaffoldNetwork ...................... Passed 0.49 sec +test 223 + Start 223: testSimDivPickers + +223: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers +223: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers +223: Test timeout computed to be: 1500 +223: [17:55:04] ------------------------------------- +223: [17:55:04] Testing github issue 1421: MaxMinPicker picking non-existent element. +223: [17:55:04] Done +223: [17:55:04] ------------------------------------- +223: [17:55:04] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +223: [17:55:04] Done +182/230 Test #223: testSimDivPickers ...................... Passed 0.01 sec +test 224 + Start 224: pickersTestsCatch + +224: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch +224: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers +224: Test timeout computed to be: 1500 +115: =>start test GETAWAY custom +115: [17:55:04] test on : 365 molecules done +183/230 Test #115: testRDFcustom .......................... Passed 4.68 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-x86_64-linux-gnu/Code/SimDivPickers/Wrap +225: Test timeout computed to be: 1500 +158: file testGithub4764.sz3.png gave hash 3374802290U not the expected 148503574U +158: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U +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 +184/230 Test #215: pyAbbreviations ........................ Passed 0.42 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-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap +226: Test timeout computed to be: 1500 +158: file github5383_1.svg gave hash 4241964660U not the expected 3666750661U +158: file github5383_2.svg gave hash 2560846108U not the expected 0U +158: file github5383_1.png gave hash 2818284953U not the expected 992803933U +213: ... +213: ---------------------------------------------------------------------- +213: Ran 3 tests in 0.015s +213: +213: OK +158: file acs1996_1.png gave hash 342575424U not the expected 2957839025U +158: file acs1996_2.svg gave hash 908745273U not the expected 1521279517U +158: file acs1996_2.png gave hash 496998965U not the expected 2664798808U +158: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +158: file acs1996_5.svg gave hash 3624853279U not the expected 1680320774U +158: file acs1996_8.svg gave hash 4110469272U not the expected 2477908768U +158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U +224: Randomness seeded to: 999542234 +224: =============================================================================== +224: All tests passed (21267 assertions in 1 test case) +224: +185/230 Test #224: pickersTestsCatch ...................... Passed 0.11 sec +test 227 + Start 227: testChemicalFeatures + +227: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures +227: Test timeout computed to be: 1500 +158: [17:55:04] 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. +227: ----------------------------------------- +227: Test1 +227: Done +186/230 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-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap +228: Test timeout computed to be: 1500 +217: ....... +217: ---------------------------------------------------------------------- +217: Ran 7 tests in 0.189s +217: +217: OK +158: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U +187/230 Test #213: pyMolEnumerator ........................ Passed 0.60 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 +203: [17:55:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached +188/230 Test #217: pyGeneralizedSubstruct ................. Passed 0.54 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 +158: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +158: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 5.215s +12: +12: OK +158: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U +158: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U +158: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U +226: ..[17:55:05] +226: +226: **** +158: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U +226: Invariant Violation +226: Can't rank more bits than the ensemble size +226: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +226: Failed Expression: num <= dp_maskBits->getNumOnBits() +226: ---------- +226: Stacktrace: +226: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +226: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +226: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 +226: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +226: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +226: 6# 0x00007FBD9345262C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +226: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-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-x86_64-linux-gnu/rdkit/rdBase.so +226: 9# 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-x86_64-linux-gnu/rdkit/rdBase.so +226: 10# 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-x86_64-linux-gnu/rdkit/rdBase.so +226: 11# 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-x86_64-linux-gnu/rdkit/rdBase.so +226: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +226: 13# 0x00007FBD9344F3C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +226: 14# _PyObject_MakeTpCall in /usr/bin/python3 +226: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 16# 0x0000000000546E76 in /usr/bin/python3 +226: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 18# _PyObject_Call_Prepend in /usr/bin/python3 +226: 19# 0x000000000059D6E4 in /usr/bin/python3 +226: 20# _PyObject_MakeTpCall in /usr/bin/python3 +226: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 22# 0x0000000000546E76 in /usr/bin/python3 +226: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 24# _PyObject_Call_Prepend in /usr/bin/python3 +226: 25# 0x000000000059D6E4 in /usr/bin/python3 +226: 26# _PyObject_MakeTpCall in /usr/bin/python3 +226: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 28# 0x0000000000546E76 in /usr/bin/python3 +226: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 30# _PyObject_Call_Prepend in /usr/bin/python3 +226: 31# 0x000000000059D6E4 in /usr/bin/python3 +226: 32# _PyObject_MakeTpCall in /usr/bin/python3 +226: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 34# _PyObject_Call_Prepend in /usr/bin/python3 +226: 35# 0x000000000059810D in /usr/bin/python3 +226: 36# 0x0000000000593E22 in /usr/bin/python3 +226: 37# _PyObject_MakeTpCall in /usr/bin/python3 +226: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +226: 39# PyEval_EvalCode in /usr/bin/python3 +226: 40# 0x00000000005FFE7F in /usr/bin/python3 +226: 41# 0x00000000006A59F2 in /usr/bin/python3 +226: 42# _PyRun_SimpleFileObject in /usr/bin/python3 +226: 43# _PyRun_AnyFileObject in /usr/bin/python3 +226: 44# Py_RunMain in /usr/bin/python3 +226: 45# Py_BytesMain in /usr/bin/python3 +226: 46# 0x00007FBD95C83D68 in /lib/x86_64-linux-gnu/libc.so.6 +226: 47# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +226: 48# _start in /usr/bin/python3 +226: ---------- +226: **** +226: +226: ... +226: ---------------------------------------------------------------------- +226: Ran 5 tests in 0.026s +226: +226: OK +158: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U +185: .................... +185: ---------------------------------------------------------------------- +185: Ran 20 tests in 2.179s +185: +185: OK +158: file github6504_2.svg gave hash 106020287U not the expected 2871662880U +158: file github6569_1.svg gave hash 1698514747U not the expected 116573839U +189/230 Test #12: pyBV ................................... Passed 5.49 sec +158: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U +225: [17:55:05] the useCache argument is deprecated and ignored +146: .[17:55:05] Molecule does not have explicit Hs. Consider calling AddHs() +190/230 Test #226: pyRanker ............................... Passed 0.39 sec +191/230 Test #185: pyRGroupDecomposition .................. Passed 2.81 sec +208: .....[17:55:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached +228: .. +228: ---------------------------------------------------------------------- +228: Ran 2 tests in 0.001s +228: +228: OK +228: Testing ChemicalFeatures Wrapper code: +192/230 Test #199: molStandardizeTest ..................... Passed 1.33 sec +169: Randomness seeded to: 4036477400 +169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +193/230 Test #228: pyFeatures ............................. Passed 0.42 sec +225: ...[17:55:05] the useCache argument is deprecated and ignored +225: [17:55:05] the useCache argument is deprecated and ignored +208: [17:55:05] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +225: .[17:55:05] the useCache argument is deprecated and ignored +158: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U +158: file AtropManyChiralsEnhanced.svg gave hash 3759358369U not the expected 348414093U +158: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U +222: ..... +222: ---------------------------------------------------------------------- +222: Ran 5 tests in 0.343s +222: +222: OK +230: ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. +219: .. +219: ---------------------------------------------------------------------- +219: Ran 2 tests in 0.518s +219: +219: OK +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) +203: [17:55:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached +194/230 Test #222: pyMatCalc .............................. Passed 0.74 sec +191: ....................[17:55:05] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:05] Explicit valence for atom # 6 F, 2, is greater than permitted +191: [17:55:05] Can't kekulize mol. Unkekulized atoms: 3 4 5 +158: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U +158: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U +158: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U +158: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U +158: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U +158: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U +158: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U +158: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U +195/230 Test #219: pyMolProcessing ........................ Passed 0.94 sec +208: .[17:55:05] Tautomer enumeration stopped at 30 tautomers: canceled 208: Enumeration was canceled due to timeout (50 ms) -203: [09:08:50] Tautomer enumeration stopped at 32 tautomers: canceled +158: file testGithub_7739_1.svg gave hash 1477601334U not the expected 52079325U +196/230 Test #230: pythonSourceTests ......................***Failed 0.69 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) + +191: .................[17:55:05] 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 4066656179U not the expected 1126644226U +203: [17:55:05] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +158: file testGithub_7739_4.svg gave hash 1029970961U not the expected 9844878U +158: [17:55:05] +158: +158: **** +158: Pre-condition Violation +158: +158: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +158: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x0000561972103715 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x00005619721DC548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x00005619721DD068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x00005619721DD4E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x00005619721AF203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x00005619721AF56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x00005619720FC24E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x00007F948F433D68 in /lib/x86_64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +158: 17# 0x00005619720FC291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: [17:55:05] +158: +158: **** +158: Range Error +158: idx +158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +158: Failed Expression: 2 < 0 +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x0000561972102E82 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x00005619721DC548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x00005619721DD068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x00005619721DD4E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x00005619721AF203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x00005619721AF56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x00005619720FC24E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x00007F948F433D68 in /lib/x86_64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +158: 17# 0x00005619720FC291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: [17:55:05] +158: +158: **** +158: Range Error +158: idx +158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +158: Failed Expression: 0 < 0 +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x00005619721037E8 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x00005619721DC548 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x00005619721DD068 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x00005619721DD4E0 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x00005619721AF203 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x00005619721AF56C in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x00005619720FC24E in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x00007F948F433D68 in /lib/x86_64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +158: 17# 0x00005619720FC291 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: =============================================================================== +158: All tests passed (6801 assertions in 105 test cases) +158: +197/230 Test #158: moldraw2DTestCatch ..................... Passed 4.78 sec +209: Randomness seeded to: 3994784667 +209: =============================================================================== +209: All tests passed (269 assertions in 19 test cases) +209: +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +161: [17:55:05] The provided InitialSeed is not an MCS and will be ignored +198/230 Test #209: testScaffoldNetwork .................... Passed 1.59 sec +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Test unfolded version of RDKFP +126: [17:55:05] ------------------------------------- +126: [17:55:05] 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: [17:55:05] ------------------------------------- +126: [17:55:05] Single atoms setting radius 1 bits in Morgan fingerprints +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #879: Pattern fingerprint should set bits for single-atom fragments. +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use AtomPairGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #2115: BitInfo not complete for RDKFingerprint +126: [17:55:05] done +126: [17:55:05] ------------------------------------- +126: [17:55:05] Github #3723: Fingerprint crash for mols with Zero order bonds +126: [17:55:05] done +199/230 Test #126: testFingerprints ....................... Passed 5.45 sec +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +148: processing +148: launch :0 +148: launch :1 +148: launch :2 +148: launch :3 +27: All 191 tests passed +144: validating reference data +203: [17:55:06] Tautomer enumeration stopped at 35 tautomers: canceled 203: Enumeration was canceled due to timeout (50 ms) -182: bulk, no symmetry +182: iterative +179: [17:55:06] ------------------------------------- +179: [17:55:06] testing PatternHolder +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +229: ============================= test session starts ============================== +229: platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 +229: rootdir: /build/reproducible-path/rdkit-202409.2/Projects +229: configfile: pytest.ini +229: plugins: typeguard-4.4.1 +229: collected 12 items +229: +179: [17:55:06] ------------------------------------- +179: [17:55:06] testing TautomerPatternHolder +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 11 tests in 1.658s +225: +225: OK +162: ........................................[17:55:06] The provided InitialSeed is not an MCS and will be ignored +162: [17:55:06] The provided InitialSeed is not an MCS and will be ignored +162: [17:55:06] The provided InitialSeed is not an MCS and will be ignored +200/230 Test #225: pySimDivPickers ........................ Passed 2.09 sec +162: .[17:55:06] The provided InitialSeed is not an MCS and will be ignored +162: [17:55:06] The provided InitialSeed is not an MCS and will be ignored +179: [17:55:06] ------------------------------------- +179: [17:55:06] testSegFaultInHolder +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: +179: [17:55:06] [17:55:06] SMILES Parse Error: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] [17:55:06] [17:55:06] [17:55:06] SMILES Parse Error: [17:55:06] [17:55:06] SMILES Parse Error: [17:55:06] SMILES Parse Error: syntax error[17:55:06] [17:55:06] syntax error while parsing: SMILES Parse Error: while parsing: syntax error while parsing: SMILES Parse Error: dsafsdfsyntax error[17:55:06] while parsing: [17:55:06] dsafsdfSMILES Parse Error: [17:55:06] dsafsdfSMILES Parse Error: +179: [17:55:06] syntax errorsyntax errorSMILES Parse Error: while parsing: [17:55:06] while parsing: syntax errordsafsdfSMILESsyntax errordsafsdfSMILES Parse Error: +179: syntax error while parsing: while parsing: while parsing: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: dsafsdf +179: dsafsdfdsafsdf[17:55:06] SMILES Parse Error: SMILES Parse Error: +179: [17:55:06] +179: SMILES Parse Error: [17:55:06] dsafsdfSMILES Parse Error: [17:55:06] [17:55:06] Failed parsing SMILES 'dsafsdf' +179: +179: syntax error[17:55:06] while parsing: dsafsdf +179: Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:06] Failed parsing SMILES 'dsafsdf'SMILESSMILES Parse Error: [17:55:06] Parse Error: SMILESFailed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'dsafsdfFailed parsing SMILES 'dsafsdf''[17:55:06] syntax error[17:55:06] [17:55:06] SMILES Parse Error: [17:55:06] syntax errorSMILESSMILESSMILES +179: SMILESsyntax errorSMILES Parse Error: for input: ' for input: 'dsafsdf' Parse Error: +179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: 'Failed parsing SMILES 'dsafsdf'syntax error Parse Error: while parsing: while parsing: [17:55:06] SMILES Parse Error: syntax errordsafsdfdsafsdf while parsing: while parsing: dsafsdf[17:55:06] ' for input: 'SMILES Parse Error: dsafsdfsyntax error while parsing: dsafsdf' +179: dsafsdf[17:55:06] 'SMILES +179: Failed parsing SMILES 'dsafsdf' +179: Parse Error: Parse Error: +179: syntax error for input: ' +179: dsafsdf'Failed parsing SMILES 'dsafsdf''Failed parsing SMILES 'dsafsdf' +179: for input: ' for input: ' +179: [17:55:06] while parsing: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf for input: '[17:55:06] [17:55:06] SMILES Parse Error: dsafsdf +179: dsafsdf +179: ' +179: Failed parsing SMILES 'dsafsdf'dsafsdf +179: [17:55:06] SMILES Parse Error: for input: 'SMILES'dsafsdf[17:55:06] +179: dsafsdf while parsing: ' +179: Parse Error: [17:55:06] +179: dsafsdfSMILES' +179: dsafsdf +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: for input: '[17:55:06] dsafsdf'SMILESFailed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +179: for input: ' +179: dsafsdf[17:55:06] Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: for input: 'dsafsdf''syntax error +179: 'dsafsdf +179: while parsing: dsafsdf' +179: +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: dsafsdf' +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: SMILES Parse Error: syntax error +179: [17:55:06] +179: SMILES Parse Error: syntax error while parsing: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: for input: 'dsafsdf' +179: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax errordsafsdf +179: while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf[17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error[17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:06] [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:06] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:06] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +162: [17:55:06] The provided InitialSeed is not an MCS and will be ignored +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] [17:55:07] [17:55:07] [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: [17:55:07] [17:55:07] SMILES Parse Error: syntax error[17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] [17:55:07] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: [17:55:07] [17:55:07] SMILES Parse Error: syntax error while parsing: while parsing: dsafsdf +179: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:07] for input: 'dsafsdf' +179: [17:55:07] [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [17:55:07] [17:55:07] [17:55:07] SMILES Parse Error: [17:55:07] [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error[17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf[17:55:07] SMILES[17:55:07] SMILES Parse Error: [17:55:07] SMILES Parse Error: SMILES Parse Error: SMILESsyntax error Parse Error: Failed parsing SMILES 'dsafsdf' while parsing: dsafsdf +179: Parse Error: for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: while parsing: dsafsdf +179: syntax errorsyntax error while parsing: [17:55:07] SMILES Parse Error: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [17:55:07] syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[17:55:07] syntax errorsyntax errorsyntax error[17:55:07] Parse Error: syntax errordsafsdf[17:55:07] [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error for input: ' +179: [17:55:07] +179: [17:55:07] SMILES for input: ' while parsing: SMILES Parse Error: dsafsdfsyntax error[17:55:07] Failed parsing SMILES 'dsafsdf'SMILES while parsing: for input: ' while parsing: for input: 'dsafsdfdsafsdfdsafsdfSMILES Parse Error: [17:55:07] 'SMILES Parse Error: Parse Error: syntax errorSMILES Parse Error: dsafsdf' while parsing: Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: ' +179: SMILESsyntax error while parsing: dsafsdf +179: while parsing: [17:55:07] syntax errordsafsdf while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] +179: ' +179: +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: while parsing: while parsing: dsafsdf' +179: SMILES Parse Error: syntax error +179: while parsing: dsafsdf +179: +179: [17:55:07] dsafsdf[17:55:07] [17:55:07] SMILES Parse Error: syntax errorSMILES while parsing: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: syntax error while parsing: dsafsdf +179: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +179: for input: 'dsafsdf' +179: +179: +179: syntax error[17:55:07] SMILES Parse Error: [17:55:07] [17:55:07] SMILES Parse Error: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:07] [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: Failed parsing SMILES 'dsafsdf' while parsing: for input: 'dsafsdf' +179: dsafsdf +179: +179: dsafsdfSMILES[17:55:07] SMILESSMILES Parse Error: Parse Error: '[17:55:07] +179: SMILES Parse Error: while parsing: Failed parsing SMILES 'dsafsdf'syntax error Parse Error: +179: [17:55:07] SMILESFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf Parse Error: dsafsdf +179: ' +179: while parsing: [17:55:07] Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'Failed parsing SMILES 'dsafsdf'dsafsdf' +179: dsafsdf +179: for input: ' for input: 'dsafsdfdsafsdf' +179: SMILES +179: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: ' +179: for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: syntax error[17:55:07] [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf[17:55:07] SMILES Parse Error: [17:55:07] SMILES Parse Error: syntax errorSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +162: .[17:55:07] The provided InitialSeed is not an MCS and will be ignored +179: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +162: [17:55:07] The provided InitialSeed is not an MCS and will be ignored +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +162: [17:55:07] The provided InitialSeed is not an MCS and will be ignored +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [17:55:07] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [17:55:07] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +162: .[17:55:07] The provided InitialSeed is not an MCS and will be ignored +179: [17:55:07] ------------------------------------- +179: [17:55:07] Results do not depend on numThreads +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 +162: [17:55:07] The provided InitialSeed is not an MCS and will be ignored +123: Warning: Atom Count for residue ARG64A does not match expected count +123: Warning: Atom Count for residue LYS80A does not match expected count +162: [17:55:07] The provided InitialSeed is not an MCS and will be ignored +123: Warning: Atom Count for residue GLU150A does not match expected count +123: Warning: Atom Count for residue ASN157A does not match expected count +123: =============================================================================== +123: All tests passed (515 assertions in 10 test cases) +123: +201/230 Test #123: descriptorsTestCatch ................... Passed 6.84 sec +162: ................. +162: ---------------------------------------------------------------------- +162: Ran 60 tests in 5.719s +162: +162: OK +124: Warning: Atom Count for residue GLU5A does not match expected count +124: Warning: Atom Count for residue ASN39A does not match expected count +202/230 Test #162: pyFMCS ................................. Passed 6.36 sec +124: Warning: Atom Count for residue GLU53A does not match expected count +124: Warning: Atom Count for residue ARG64A does not match expected count +124: Warning: Atom Count for residue LYS80A does not match expected count +124: Warning: Atom Count for residue GLU150A does not match expected count +124: Warning: Atom Count for residue ASN157A does not match expected count +124: .[17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: .[17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: ..[17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: .[17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ...[17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: [17:55:07] DEPRECATION WARNING: please use MorganGenerator +124: ....[17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: ....[17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: [17:55:07] DEPRECATION WARNING: please use AtomPairGenerator +124: .[17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ..[17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: .[17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [17:55:07] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ... +124: ---------------------------------------------------------------------- +124: Ran 31 tests in 6.476s +124: +124: OK +124: exactmw 78.046950192 +124: amw 78.11399999999999 +124: lipinskiHBA 0.0 +124: lipinskiHBD 0.0 +124: NumRotatableBonds 0.0 +124: NumHBD 0.0 +124: NumHBA 0.0 +124: NumHeavyAtoms 6.0 +124: NumAtoms 6.0 +124: NumHeteroatoms 0.0 +124: NumAmideBonds 0.0 +124: FractionCSP3 0.0 +124: NumRings 1.0 +124: NumAromaticRings 1.0 +124: NumAliphaticRings 0.0 +124: NumSaturatedRings 0.0 +124: NumHeterocycles 0.0 +124: NumAromaticHeterocycles 0.0 +124: NumSaturatedHeterocycles 0.0 +124: NumAliphaticHeterocycles 0.0 +124: NumSpiroAtoms 0.0 +124: NumBridgeheadAtoms 0.0 +124: NumAtomStereoCenters 0.0 +124: NumUnspecifiedAtomStereoCenters 0.0 +124: labuteASA 37.43140311949697 +124: tpsa 0.0 +124: CrippenClogP 1.6866 +124: CrippenMR 26.441999999999993 +124: chi0v 3.464101615137755 +124: chi1v 2.0000000000000004 +124: chi2v 0.6666666666666671 +124: chi3v 0.6666666666666671 +124: chi4v 0.38490017945975075 +124: chi0n 3.464101615137755 +124: chi1n 2.0000000000000004 +124: chi2n 0.6666666666666671 +124: chi3n 0.6666666666666671 +124: chi4n 0.38490017945975075 +124: hallKierAlpha -0.78 +124: kappa1 3.4115708812260532 +124: kappa2 1.6057694396735218 +124: kappa3 0.5823992601400448 +124: Phi 0.9130327103921437 +124: exactmw 78.046950192 +124: lipinskiHBA 0.0 +208: Enumeration has completed 203: 375 203: Enumeration has completed -182: [09:08:52] Relabelling existing label -203: [09:08:52] Tautomer enumeration stopped at 67 tautomers: canceled -150: ...[09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() -150: [09:08:52] Molecule does not have explicit Hs. Consider calling AddHs() +203/230 Test #124: pyMolDescriptors ....................... Passed 7.30 sec +208: [17:55:07] Tautomer enumeration stopped at 40 tautomers: canceled +203: [17:55:07] Tautomer enumeration stopped at 35 tautomers: canceled +182: bulk +218: Randomness seeded to: 2663938878 +218: =============================================================================== +218: All tests passed (203 assertions in 1 test case) +218: +204/230 Test #218: testMolProcessing ...................... Passed 3.41 sec +208: ..........[17:55:07] Explicit valence for atom # 1 N, 4, is greater than permitted +208: [17:55:07] Explicit valence for atom # 1 N, 4, is greater than permitted +208: [17:55:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208: [17:55:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [17:55:08] Finished: testSmiCorrectness() +73: [17:55:08] ----------------------------------------- +73: +73: [17:55:08] +73: ----------------------------------------- +73: [17:55:08] Property will be truncated after the first blank line +73: [17:55:08] [17:55:08] Property will be truncated after the first blank line +73: Spurious data before the first property will be ignored +73: [17:55:08] Property will be truncated after the first blank line +144: processing +144: launch :0 +144: launch :1 +144: launch :2 +144: launch :3 +73: [17:55:08] Finished: testSDCorrectness() +73: [17:55:08] ----------------------------------------- +73: +205/230 Test #73: testMultithreadedMolSupplier ........... Passed 8.83 sec +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 +208: ............[17:55:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208: [17:55:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +208: [17:55:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +206/230 Test #203: molTautomerTest ........................ Passed 5.08 sec +208: ........[17:55:09] Explicit valence for atom # 1 O, 3, is greater than permitted +208: . +208: ---------------------------------------------------------------------- +208: Ran 37 tests in 4.637s +208: +208: OK +208: done +207/230 Test #208: pyMolStandardize ....................... Passed 5.06 sec +157: Done +157: ----------------- Test Github #781: Rendering single-atom molecules +157: Done +157: ----------------- Test 3 +157: file test3_1.png gave hash 1514877476U not the expected 3984824963U +157: file test3_2.png gave hash 895995063U not the expected 238321316U +208/230 Test #195: pyTestThreads .......................... Passed 6.10 sec +157: file test3_3.png gave hash 2806558077U not the expected 414888185U +157: file test3_4.png gave hash 3204576434U not the expected 2265825690U +157: file test3_5.png gave hash 3784843232U not the expected 1911551403U +157: file test3_6.png gave hash 2648864811U not the expected 577293879U +157: file test3_7.png gave hash 727952731U not the expected 248355372U +157: Done +157: ----------------- Test Github774: upside-down drawings +157: file test774_1.png gave hash 1746502640U not the expected 927423591U +157: file test774_2.png gave hash 1057482804U not the expected 1171827286U +157: Done +157: ----------------- Test 9 (molecule legends) +157: file test9_1.svg gave hash 923579170U not the expected 1484349178U +157: Done +157: ----------------- Test Github852: Lines used to wedge bonds are too thick +157: file test852_1.png gave hash 3083219870U not the expected 736085072U +157: file test852_2.png gave hash 1999141294U not the expected 1438089260U +157: ---------------- +157: ---------------- +157: ---------------- +157: ---------------- +157: Done +157: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +157: file test860_1.png gave hash 667708706U not the expected 2065140854U +157: file test860_2.png gave hash 2350165565U not the expected 3098360765U +157: file test860_3.png gave hash 3798998670U not the expected 3439618110U +157: Done +157: ----------------- Test Github #910: ugly coordinates generated for peptide chains +157: Done +157: ----------------- Test Github #932: mistake in SVG for wedged bonds +157: Done +157: ----------------- Test Github #953: default color should not be cyan +157: Done +157: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +157: Done +157: ----------------- Test Deuterium, Tritium +157: Done +157: ----------------- Test crossed bonds +157: Done +157: ----------------- Testing drawing a second molecule +157: Done +157: ----------------- Testing drawing a grid of molecules +157: Done +157: ----------------- Testing drawMolecules +157: file test12_1.svg gave hash 2982175789U not the expected 881731720U +157: Done +157: ----------------- Test JSON Configuration +157: Done +157: ----------------- Testing github 1090: escape html characters in SVG output +157: Done +157: ----------------- Testing github 1035: overflow bug in SVG color generation +157: Done +157: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes +157: Done +157: ----------------- Testing github 1322: add custom atom labels +157: Done +157: ----------------- Testing use of a black & white palette +157: Done +157: ----------------- Testing use of continuous highlighting with drawMolecules +157: Done +157: ----------------- Test 17 - Testing maximum font size +157: Done +157: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list +157: Done +157: ----------------- Testing use of fixed scales for drawing. +157: Done +157: ----------------- Testing rotation of 2D drawing. +157: Done +157: ----------------- Testing inclusion of molecule metadata +157: Done +157: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default +157: Done +157: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions +157: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U +157: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U +157: Done +157: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn +157: Done +157: ----------------- Testing testGithub2931: multi-coloured molecule highlights. +157: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U +157: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U +157: Done +157: ----------------- Testing annotation of 2D Drawing. +157: file test20_1.png gave hash 2978996523U not the expected 1672353490U +157: file test20_2.png gave hash 745058850U not the expected 1073213605U +157: file test20_3.png gave hash 472521001U not the expected 471234756U +157: file test20_4.png gave hash 1015859242U not the expected 2803490234U +157: Done +157: ----------------- Test 21 - different font +157: Done +157: ----------------- Test 22 - draw explicit methyls. +157: Done +157: ----------------- Testing drawing of legends. +157: Done +157: ----------------- Test Github 3305 - change and scale line widths. +157: file testGithub3305_1.png gave hash 588173490U not the expected 1801411420U +157: file testGithub3305_2.png gave hash 3393765154U not the expected 2904846519U +157: file testGithub3305_3.png gave hash 694090236U not the expected 2915229647U +157: file testGithub3305_4.png gave hash 3784843232U not the expected 1911551403U +157: file testGithub3305_5.png gave hash 2382054754U not the expected 614319597U +157: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U +157: file testGithub3305_6.png gave hash 1247498295U not the expected 3926947401U +157: file testGithub3305_7.png gave hash 3628125988U not the expected 1720405002U +157: Done +157: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. +157: Done +157: ----------------- Test Github 4156 - bad scale for radicals in grid +157: Done +157: ----------------- Test JSON atomColourPalette +157: Done +157: ----------------- Test draw aromatic OR queries +157: Done +157: ----------------- Test AND queries +157: Done +209/230 Test #157: moldraw2DTest1 ......................... Passed 8.96 sec +182: bulk, no symmetry +179: [17:55:10] ------------------------------------- +179: [17:55:10] Results do not depend on numThreads (all same) +179: [17:55:10] ------------------------------------- +179: [17:55:10] testTautomerQueries +179: [17:55:10] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +179: [17:55:10] ------------------------------------- +179: [17:55:10] github3881 recursive smarts with rings +210/230 Test #179: substructLibraryTest ................... Passed 8.40 sec +181: ......[17:55:10] +181: +181: **** +181: Pre-condition Violation +181: RingInfo not initialized +181: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +181: Failed Expression: df_init +181: ---------- +181: Stacktrace: +181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +181: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 12# 0x00007F2E7DA552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 14# 0x00007F2E8057E62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 17# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 18# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +181: 19# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 20# 0x00007F2E7D9AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 21# 0x00007F2E7D9AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 22# 0x00007F2E7D9AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 23# 0x00007F2E7D9AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 24# 0x00007F2E7D9AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 26# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 27# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 28# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 30# 0x00007F2E8057B3C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 31# _PyObject_MakeTpCall in /usr/bin/python3 +181: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 33# 0x0000000000546E76 in /usr/bin/python3 +181: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 35# _PyObject_Call_Prepend in /usr/bin/python3 +181: 36# 0x000000000059D6E4 in /usr/bin/python3 +181: 37# _PyObject_MakeTpCall in /usr/bin/python3 +181: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 39# 0x0000000000546E76 in /usr/bin/python3 +181: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 41# _PyObject_Call_Prepend in /usr/bin/python3 +181: 42# 0x000000000059D6E4 in /usr/bin/python3 +181: 43# _PyObject_MakeTpCall in /usr/bin/python3 +181: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 45# 0x0000000000546E76 in /usr/bin/python3 +181: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 47# _PyObject_Call_Prepend in /usr/bin/python3 +181: 48# 0x000000000059D6E4 in /usr/bin/python3 +181: 49# _PyObject_MakeTpCall in /usr/bin/python3 +181: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 51# _PyObject_Call_Prepend in /usr/bin/python3 +181: 52# 0x000000000059810D in /usr/bin/python3 +181: 53# 0x0000000000593E22 in /usr/bin/python3 +181: 54# _PyObject_MakeTpCall in /usr/bin/python3 +181: 55# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 56# PyEval_EvalCode in /usr/bin/python3 +181: 57# 0x00000000005FFE7F in /usr/bin/python3 +181: 58# 0x00000000006A59F2 in /usr/bin/python3 +181: 59# _PyRun_SimpleFileObject in /usr/bin/python3 +181: 60# _PyRun_AnyFileObject in /usr/bin/python3 +181: 61# Py_RunMain in /usr/bin/python3 +181: 62# Py_BytesMain in /usr/bin/python3 +181: 63# 0x00007F2E80D26D68 in /lib/x86_64-linux-gnu/libc.so.6 +181: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +181: 65# _start in /usr/bin/python3 +181: ---------- +181: **** +181: +181: [17:55:10] +181: +181: **** +181: Pre-condition Violation +181: RingInfo not initialized +181: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +181: Failed Expression: df_init +181: ---------- +181: Stacktrace: +181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 3# 0x00007F2E7D4E5020 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 13# 0x00007F2E7DA552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 15# 0x00007F2E8057E62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 17# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 18# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 19# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +181: 20# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 21# 0x00007F2E7D9AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 22# 0x00007F2E7D9AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 23# 0x00007F2E7D9AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 24# 0x00007F2E7D9AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 25# 0x00007F2E7D9AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +181: 26# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 27# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 28# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 29# 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-x86_64-linux-gnu/rdkit/rdBase.so +181: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 31# 0x00007F2E8057B3C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +181: 32# _PyObject_MakeTpCall in /usr/bin/python3 +181: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 34# 0x0000000000546E76 in /usr/bin/python3 +181: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 36# _PyObject_Call_Prepend in /usr/bin/python3 +181: 37# 0x000000000059D6E4 in /usr/bin/python3 +181: 38# _PyObject_MakeTpCall in /usr/bin/python3 +181: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 40# 0x0000000000546E76 in /usr/bin/python3 +181: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 42# _PyObject_Call_Prepend in /usr/bin/python3 +181: 43# 0x000000000059D6E4 in /usr/bin/python3 +181: 44# _PyObject_MakeTpCall in /usr/bin/python3 +181: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 46# 0x0000000000546E76 in /usr/bin/python3 +181: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 48# _PyObject_Call_Prepend in /usr/bin/python3 +181: 49# 0x000000000059D6E4 in /usr/bin/python3 +181: 50# _PyObject_MakeTpCall in /usr/bin/python3 +181: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 52# _PyObject_Call_Prepend in /usr/bin/python3 +181: 53# 0x000000000059810D in /usr/bin/python3 +181: 54# 0x0000000000593E22 in /usr/bin/python3 +181: 55# _PyObject_MakeTpCall in /usr/bin/python3 +181: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 57# PyEval_EvalCode in /usr/bin/python3 +181: 58# 0x00000000005FFE7F in /usr/bin/python3 +181: 59# 0x00000000006A59F2 in /usr/bin/python3 +181: 60# _PyRun_SimpleFileObject in /usr/bin/python3 +181: 61# _PyRun_AnyFileObject in /usr/bin/python3 +181: 62# Py_RunMain in /usr/bin/python3 +181: 63# Py_BytesMain in /usr/bin/python3 +181: 64# 0x00007F2E80D26D68 in /lib/x86_64-linux-gnu/libc.so.6 +181: 65# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +181: 66# _start in /usr/bin/python3 +181: ---------- +181: **** +181: +182: [17:55:10] Relabelling existing label +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +79: =============================================================================== +79: All tests passed (1586 assertions in 98 test cases) +79: +211/230 Test #79: fileParsersCatchTest ................... Passed 10.91 sec +27: All 191 tests passed +182: Best mapping +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +212/230 Test #182: testRGroupDecomp ....................... Passed 8.73 sec 173: VS001: PASSED 173: VS002: PASSED 173: VS003: PASSED @@ -33721,415 +34304,26 @@ 173: VS300: PASSED 173: Check finished: 0 molecules failed. 173: Failed: -182: Best mapping -189/230 Test #173: pyCIPLabelsValidation .................. Passed 16.83 sec -test 209 - Start 209: testScaffoldNetwork - -209: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -209: Test timeout computed to be: 1500 -150: ... -150: ---------------------------------------------------------------------- -150: Ran 19 tests in 28.907s -150: -150: OK -150: Testing MolAlign Wrappers -190/230 Test #150: pyMolAlign ............................. Passed 29.89 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -210: Test timeout computed to be: 1500 -208: Enumeration has completed -191/230 Test #182: testRGroupDecomp ....................... Passed 13.91 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -211: Test timeout computed to be: 1500 -208: [09:08:53] Tautomer enumeration stopped at 42 tautomers: canceled -208: ..........[09:08:53] Explicit valence for atom # 1 N, 4, is greater than permitted -208: [09:08:53] Explicit valence for atom # 1 N, 4, is greater than permitted -208: [09:08:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -208: [09:08:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -179: [09:08:53] ------------------------------------- -179: [09:08:53] Results do not depend on numThreads (all same) -179: [09:08:53] ------------------------------------- -179: [09:08:53] testTautomerQueries -179: [09:08:53] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -179: [09:08:53] ------------------------------------- -179: [09:08:53] github3881 recursive smarts with rings -192/230 Test #179: substructLibraryTest ................... Passed 15.85 sec -test 212 - Start 212: testMolEnumerator - -212: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -212: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator -212: Test timeout computed to be: 1500 -211: . -211: ---------------------------------------------------------------------- -211: Ran 1 test in 0.053s -211: -211: OK -212: Randomness seeded to: 2948331540 -212: [09:08:54] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -210: ....... -210: ---------------------------------------------------------------------- -210: Ran 7 tests in 0.104s -210: -210: OK -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 -212: =============================================================================== -212: All tests passed (321 assertions in 16 test cases) -212: -193/230 Test #212: testMolEnumerator ...................... Passed 0.12 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-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap -213: Test timeout computed to be: 1500 -194/230 Test #210: pyScaffoldNetwork ...................... Passed 1.30 sec -test 214 - Start 214: testAbbreviations - -214: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations -214: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations -214: Test timeout computed to be: 1500 -214: Randomness seeded to: 4263323965 -214: [09:08:54] SMARTS Parse Error: syntax error while parsing: *fail -214: [09:08:54] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -195/230 Test #211: pyScaffoldNetworkPickling .............. Passed 1.32 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-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap -215: Test timeout computed to be: 1500 -214: [09:08:54] no suitable SubstanceGroups found -214: =============================================================================== -214: All tests passed (195 assertions in 12 test cases) -214: -213: ... -213: ---------------------------------------------------------------------- -213: Ran 3 tests in 0.019s -213: -213: OK -196/230 Test #203: molTautomerTest ........................ Passed 7.32 sec -197/230 Test #214: testAbbreviations ...................... Passed 0.36 sec -test 216 - Start 216: generalizedSubstructCatch - -216: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -216: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -216: Test timeout computed to be: 1500 -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-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -217: Test timeout computed to be: 1500 -198/230 Test #213: pyMolEnumerator ........................ Passed 0.54 sec -test 218 - Start 218: testMolProcessing - -218: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing -218: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing -218: Test timeout computed to be: 1500 -216: Randomness seeded to: 655562480 -216: =============================================================================== -216: All tests passed (486 assertions in 10 test cases) -216: -199/230 Test #216: generalizedSubstructCatch .............. Passed 0.39 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-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap -219: Test timeout computed to be: 1500 -209: Randomness seeded to: 1616884633 -209: =============================================================================== -209: All tests passed (269 assertions in 19 test cases) -209: -200/230 Test #209: testScaffoldNetwork .................... Passed 2.27 sec -test 220 - Start 220: testQuery - -220: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query/testQuery -220: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/Query -220: Test timeout computed to be: 1500 -220: Query -220: Query2 -220: Equality -220: Greater -220: GreaterEqual -220: Less -220: LessEqual -220: Open Range -220: Closed Range -220: Float -220: With Tolerance -220: Set -220: And -220: Or -220: XOr -220: pointer and copy foo -220: Set2 -201/230 Test #220: testQuery .............................. Passed 0.01 sec -test 221 - Start 221: testMatCalc - -221: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -221: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc -221: Test timeout computed to be: 1500 -221: 1.68022e+08 -221: 1.73149e+08 -221: 1.05549e+08 -221: 7.20603e+07 -221: 1.41535e+08 -221: 1.08592e+08 -221: 1.11334e+08 -221: 2.05553e+08 -221: 1.54962e+08 -221: 8.08231e+07 -221: 5.61421e+07 -221: 1.28874e+08 -221: 1.59011e+08 -221: 8.69902e+07 -221: 1.31367e+08 -221: 2.27389e+08 -221: 1.60289e+08 -221: 7.79813e+07 -221: 1.61001e+08 -221: 2.07599e+08 -221: 2.24432e+08 -221: 1.39725e+08 -221: 2.42614e+08 -221: 1.77578e+08 -221: 1.05908e+08 -221: 9.06742e+07 -221: 1.8087e+08 -221: 1.98182e+08 -221: 2.03052e+08 -221: 1.7673e+08 -221: 9.32798e+07 -221: 1.37969e+08 -221: 1.83778e+08 -221: 2.1228e+08 -221: 5.06157e+07 -221: 1.566e+08 -221: 2.37142e+08 -221: 1.49345e+08 -221: 7.05819e+07 -221: 1.71633e+08 -221: 1.96817e+08 -221: 2.18246e+08 -221: 9.49496e+07 -221: 2.25618e+08 -221: 1.30219e+08 -202/230 Test #221: testMatCalc ............................ Passed 0.01 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-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -222: Test timeout computed to be: 1500 -215: ....... -215: ---------------------------------------------------------------------- -215: Ran 7 tests in 0.026s -215: -215: OK -203/230 Test #215: pyAbbreviations ........................ Passed 0.85 sec -test 223 - Start 223: testSimDivPickers - -223: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers -223: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers -223: Test timeout computed to be: 1500 -223: [09:08:55] ------------------------------------- -223: [09:08:55] Testing github issue 1421: MaxMinPicker picking non-existent element. -223: [09:08:55] Done -223: [09:08:55] ------------------------------------- -223: [09:08:55] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -223: [09:08:55] Done -204/230 Test #223: testSimDivPickers ...................... Passed 0.03 sec -test 224 - Start 224: pickersTestsCatch - -224: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch -224: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/SimDivPickers -224: Test timeout computed to be: 1500 -217: ....... -217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.233s -217: -217: OK -205/230 Test #217: pyGeneralizedSubstruct ................. Passed 1.07 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-x86_64-linux-gnu/Code/SimDivPickers/Wrap -225: Test timeout computed to be: 1500 -208: ............[09:08:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -208: [09:08:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -208: [09:08:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -224: Randomness seeded to: 1181784601 -224: =============================================================================== -224: All tests passed (21267 assertions in 1 test case) -224: -206/230 Test #224: pickersTestsCatch ...................... Passed 0.24 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-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap -226: Test timeout computed to be: 1500 -222: ..... -222: ---------------------------------------------------------------------- -222: Ran 5 tests in 0.429s -222: -222: OK -208: ........[09:08:56] Explicit valence for atom # 1 O, 3, is greater than permitted -208: . -208: ---------------------------------------------------------------------- -208: Ran 37 tests in 7.060s -208: -208: OK -208: done -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 29.27 seconds -207/230 Test #161: testFMCS ............................... Passed 29.35 sec -test 227 - Start 227: testChemicalFeatures - -227: Test command: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/Code/ChemicalFeatures -227: Test timeout computed to be: 1500 -226: ..[09:08:56] -226: -226: **** -226: Invariant Violation -226: Can't rank more bits than the ensemble size -226: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -226: Failed Expression: num <= dp_maskBits->getNumOnBits() -226: ---------- -226: Stacktrace: -226: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -226: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -226: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 -226: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-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-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -226: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -226: 6# 0x00007F89A78F362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -226: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-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-x86_64-linux-gnu/rdkit/rdBase.so -226: 9# 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-x86_64-linux-gnu/rdkit/rdBase.so -226: 10# 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-x86_64-linux-gnu/rdkit/rdBase.so -226: 11# 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-x86_64-linux-gnu/rdkit/rdBase.so -226: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -226: 13# 0x00007F89A78F03C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -226: 14# _PyObject_MakeTpCall in /usr/bin/python3 -226: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 16# 0x0000000000546E76 in /usr/bin/python3 -226: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 18# _PyObject_Call_Prepend in /usr/bin/python3 -226: 19# 0x000000000059D6E4 in /usr/bin/python3 -226: 20# _PyObject_MakeTpCall in /usr/bin/python3 -226: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 22# 0x0000000000546E76 in /usr/bin/python3 -226: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 24# _PyObject_Call_Prepend in /usr/bin/python3 -226: 25# 0x000000000059D6E4 in /usr/bin/python3 -226: 26# _PyObject_MakeTpCall in /usr/bin/python3 -226: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 28# 0x0000000000546E76 in /usr/bin/python3 -226: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 30# _PyObject_Call_Prepend in /usr/bin/python3 -226: 31# 0x000000000059D6E4 in /usr/bin/python3 -226: 32# _PyObject_MakeTpCall in /usr/bin/python3 -226: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 34# _PyObject_Call_Prepend in /usr/bin/python3 -226: 35# 0x000000000059810D in /usr/bin/python3 -226: 36# 0x0000000000593E22 in /usr/bin/python3 -226: 37# _PyObject_MakeTpCall in /usr/bin/python3 -226: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -226: 39# PyEval_EvalCode in /usr/bin/python3 -226: 40# 0x00000000005FFE7F in /usr/bin/python3 -226: 41# 0x00000000006A59F2 in /usr/bin/python3 -226: 42# _PyRun_SimpleFileObject in /usr/bin/python3 -226: 43# _PyRun_AnyFileObject in /usr/bin/python3 -226: 44# Py_RunMain in /usr/bin/python3 -226: 45# Py_BytesMain in /usr/bin/python3 -226: 46# 0x00007F89AA159D68 in /lib/x86_64-linux-gnu/libc.so.6 -226: 47# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -226: 48# _start in /usr/bin/python3 -226: ---------- -226: **** -226: -226: ... -226: ---------------------------------------------------------------------- -226: Ran 5 tests in 0.047s -226: -226: OK -225: [09:08:56] the useCache argument is deprecated and ignored -208/230 Test #208: pyMolStandardize ....................... Passed 7.70 sec -209/230 Test #222: pyMatCalc .............................. Passed 1.23 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-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap -228: Test timeout computed to be: 1500 -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 -227: ----------------------------------------- -227: Test1 -227: Done -210/230 Test #227: testChemicalFeatures ................... Passed 0.03 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 -211/230 Test #226: pyRanker ............................... Passed 0.76 sec -225: ...[09:08:56] the useCache argument is deprecated and ignored -225: [09:08:56] the useCache argument is deprecated and ignored -225: .[09:08:56] the useCache argument is deprecated and ignored -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -219: .. -219: ---------------------------------------------------------------------- -219: Ran 2 tests in 1.050s -219: -219: OK -228: .. -228: ---------------------------------------------------------------------- -228: Ran 2 tests in 0.048s -228: -228: OK -228: Testing ChemicalFeatures Wrapper code: -212/230 Test #219: pyMolProcessing ........................ Passed 2.02 sec -213/230 Test #228: pyFeatures ............................. Passed 0.78 sec -191: ..[09:08:57] +213/230 Test #173: pyCIPLabelsValidation .................. Passed 9.69 sec +93: 0,0 0 +93: 0,1 0 +93: 1,0 0 +93: 1,1 0 +93: 2,0 0 +93: 2,1 0 +214/230 Test #93: testEnumeration ........................ Passed 11.49 sec +150: .............[17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:12] Molecule does not have explicit Hs. Consider calling AddHs() +191: ..[17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34143,7 +34337,7 @@ 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34154,17 +34348,17 @@ 191: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 @@ -34197,13 +34391,13 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 59# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [09:08:57] +191: [17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34218,7 +34412,7 @@ 191: 3# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34229,17 +34423,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -34272,13 +34466,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [09:08:57] +191: [17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34293,7 +34487,7 @@ 191: 3# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34304,17 +34498,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -34347,13 +34541,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [09:08:57] +191: [17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34368,7 +34562,7 @@ 191: 3# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34379,17 +34573,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -34422,13 +34616,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [09:08:57] +191: [17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34443,7 +34637,7 @@ 191: 3# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34454,17 +34648,17 @@ 191: 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x0000000000546E76 in /usr/bin/python3 @@ -34497,13 +34691,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 60# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: .....[09:08:57] +191: .....[17:55:12] 191: 191: **** 191: Range Error @@ -34517,7 +34711,7 @@ 191: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34528,17 +34722,17 @@ 191: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 @@ -34571,45 +34765,41 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 59# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ......[09:08:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -191: [09:08:57] ERROR: Smiles parse error on line 0 -191: [09:08:57] ERROR: Cannot create molecule from : 'c1ccccc' -191: [09:08:57] SMILES Parse Error: extra open parentheses for input: 'C(C' -191: [09:08:57] ERROR: Smiles parse error on line 3 -191: [09:08:57] ERROR: Cannot create molecule from : 'C(C' -191: [09:08:57] Explicit valence for atom # 1 C, 5, is greater than permitted -191: [09:08:57] ERROR: Could not sanitize molecule on line 6 -191: [09:08:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -191: [09:08:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -191: [09:08:57] ERROR: Smiles parse error on line 0 -191: [09:08:57] ERROR: Cannot create molecule from : 'c1ccccc' -191: [09:08:57] SMILES Parse Error: extra open parentheses for input: 'C(C' -191: [09:08:57] ERROR: Smiles parse error on line 3 -191: [09:08:57] ERROR: Cannot create molecule from : 'C(C' -191: [09:08:57] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -191: [09:08:57] ERROR: Smiles parse error on line 6 -191: [09:08:57] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -191: [09:08:57] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:57] ERROR: Could not sanitize molecule ending on line 21 -191: [09:08:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:57] ERROR: EOF hit while reading atoms -191: [09:08:57] ERROR: moving to the beginning of the next molecule -191: [09:08:57] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:57] ERROR: Could not sanitize molecule ending on line 21 -191: [09:08:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:57] ERROR: EOF hit while reading atoms -191: [09:08:57] ERROR: moving to the beginning of the next molecule -27: All 191 tests passed -27: done -27: ------------------------------------- -27: Unit tests for all MMFF constraint terms. -191: ....[09:08:57] +191: ......[17:55:12] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +191: [17:55:12] ERROR: Smiles parse error on line 0 +191: [17:55:12] ERROR: Cannot create molecule from : 'c1ccccc' +191: [17:55:12] SMILES Parse Error: extra open parentheses for input: 'C(C' +191: [17:55:12] ERROR: Smiles parse error on line 3 +191: [17:55:12] ERROR: Cannot create molecule from : 'C(C' +191: [17:55:12] Explicit valence for atom # 1 C, 5, is greater than permitted +191: [17:55:12] ERROR: Could not sanitize molecule on line 6 +191: [17:55:12] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +191: [17:55:12] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +191: [17:55:12] ERROR: Smiles parse error on line 0 +191: [17:55:12] ERROR: Cannot create molecule from : 'c1ccccc' +191: [17:55:12] SMILES Parse Error: extra open parentheses for input: 'C(C' +191: [17:55:12] ERROR: Smiles parse error on line 3 +191: [17:55:12] ERROR: Cannot create molecule from : 'C(C' +191: [17:55:12] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +191: [17:55:12] ERROR: Smiles parse error on line 6 +191: [17:55:12] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +191: [17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] ERROR: Could not sanitize molecule ending on line 21 +191: [17:55:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] ERROR: EOF hit while reading atoms +191: [17:55:12] ERROR: moving to the beginning of the next molecule +191: [17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] ERROR: Could not sanitize molecule ending on line 21 +191: [17:55:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] ERROR: EOF hit while reading atoms +191: [17:55:12] ERROR: moving to the beginning of the next molecule +191: ....[17:55:12] 191: 191: **** 191: Pre-condition Violation @@ -34623,7 +34813,7 @@ 191: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34634,17 +34824,17 @@ 191: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 @@ -34677,13 +34867,13 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 59# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ............[09:08:57] +191: ............[17:55:12] 191: 191: **** 191: Range Error @@ -34697,7 +34887,7 @@ 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x00007F21EE34362C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x00007FC5F008962C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 7# 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-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34708,17 +34898,17 @@ 191: 13# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x00007F21EB3AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x00007F21EB3AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x00007F21EB3AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x00007F21EB3AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x00007F21EB3AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x00007FC5ECFAE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x00007FC5ECFAE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x00007FC5ECFAE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x00007FC5ECFAE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x00007FC5ECFAE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 22# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 23# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 24# 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-x86_64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x00007F21EE3403C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x00007FC5F00863C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x0000000000546E76 in /usr/bin/python3 @@ -34751,13 +34941,72 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x00007F21EE8D9D68 in /lib/x86_64-linux-gnu/libc.so.6 +191: 59# 0x00007FC5F04D7D68 in /lib/x86_64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ...[09:08:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +191: ...[17:55:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +191: ............................[17:55:12] SMILES Parse Error: unclosed ring for input: 'C1CC' +191: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| +191: 747 +191: ..[17:55:12] WARNING: not removing hydrogen atom without neighbors +191: [17:55:12] WARNING: not removing hydrogen atom with dummy atom neighbors +191: [17:55:12] WARNING: not removing hydrogen atom with wedged bond +191: [17:55:12] WARNING: not removing hydrogen atom without neighbors +191: [17:55:12] WARNING: not removing hydrogen atom with dummy atom neighbors +168: Randomness seeded to: 3623935956 +168: Timed out after 11 seconds. +181: ............. +181: ---------------------------------------------------------------------- +181: Ran 19 tests in 9.767s +181: +181: OK +181: Testing atom rings +181: testing bond rings +181: searching atom rings +181: searching bond rings +181: done +215/230 Test #181: pySubstructLibrary ..................... Passed 10.30 sec +191: ......[17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: .[17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [17:55:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: [17:55:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: [17:55:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: ..........[17:55:12] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +191: [17:55:12] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +191: .[17:55:12] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +191: ..[17:55:12] SMILES Parse Error: syntax error while parsing: error +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +191: [17:55:12] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +191: [17:55:12] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +191: .........................[17:55:12] SMILES Parse Error: syntax error while parsing: garbage_0 +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +191: [17:55:12] SMILES Parse Error: syntax error while parsing: garbage_2 +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +191: [17:55:12] SMILES Parse Error: syntax error while parsing: garbage_4 +191: [17:55:12] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +191: ........... +191: ---------------------------------------------------------------------- +191: Ran 277 tests in 9.392s +191: +191: OK +191: supplier: +191: supplier: +191: supplier: +216/230 Test #191: pyGraphMolWrap ......................... Passed 10.04 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: ------------------------------------- @@ -34768,73 +35017,33 @@ 27: done 27: ------------------------------------- 27: Unit test for MMFF butane scan. -191: ............................[09:08:57] SMILES Parse Error: unclosed ring for input: 'C1CC' -191: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -191: 323 -191: ..[09:08:57] WARNING: not removing hydrogen atom without neighbors -191: [09:08:57] WARNING: not removing hydrogen atom with dummy atom neighbors -191: [09:08:57] WARNING: not removing hydrogen atom with wedged bond -191: [09:08:57] WARNING: not removing hydrogen atom without neighbors -191: [09:08:57] WARNING: not removing hydrogen atom with dummy atom neighbors +150: ...[17:55:13] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:13] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:13] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:13] Molecule does not have explicit Hs. Consider calling AddHs() +150: [17:55:13] Molecule does not have explicit Hs. Consider calling AddHs() +150: ... +150: ---------------------------------------------------------------------- +150: Ran 19 tests in 12.490s +150: +150: OK +150: Testing MolAlign Wrappers +217/230 Test #150: pyMolAlign ............................. Passed 12.85 sec 27: done -214/230 Test #27: testMMFFForceField ..................... Passed 45.01 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) -215/230 Test #230: pythonSourceTests ......................***Failed 1.83 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) - -191: ......[09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: .[09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:58] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: [09:08:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: ..........[09:08:58] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -191: .[09:08:58] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -191: ..[09:08:58] SMILES Parse Error: syntax error while parsing: error -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -191: [09:08:58] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -191: .........................[09:08:58] SMILES Parse Error: syntax error while parsing: garbage_0 -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -191: [09:08:58] SMILES Parse Error: syntax error while parsing: garbage_2 -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -191: [09:08:58] SMILES Parse Error: syntax error while parsing: garbage_4 -191: [09:08:58] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -191: ........... -191: ---------------------------------------------------------------------- -191: Ran 277 tests in 14.892s -191: -191: OK -191: supplier: -191: supplier: -191: supplier: -216/230 Test #191: pyGraphMolWrap ......................... Passed 16.14 sec -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 11 tests in 2.310s -225: -225: OK -217/230 Test #225: pySimDivPickers ........................ Passed 3.07 sec -218/230 Test #195: pyTestThreads .......................... Passed 14.23 sec -229: ============================= test session starts ============================== -229: platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 -229: rootdir: /build/reproducible-path/rdkit-202409.2/Projects -229: configfile: pytest.ini -229: plugins: typeguard-4.4.1 -229: collected 12 items -229: +218/230 Test #27: testMMFFForceField ..................... Passed 13.98 sec +50: Randomness seeded to: 4192400576 +50: =============================================================================== +50: All tests passed (14835 assertions in 14 test cases) +50: +219/230 Test #50: canonTestsCatch ........................ Passed 14.06 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 13.72 seconds +220/230 Test #161: testFMCS ............................... Passed 13.77 sec 148: --------------------------------- 148: test O3A multithreading bug 148: @@ -34842,257 +35051,94 @@ 148: testCrippenO3A multithreading 148: 148: generating reference data -181: ......[09:09:00] -181: -181: **** -181: Pre-condition Violation -181: RingInfo not initialized -181: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -181: Failed Expression: df_init -181: ---------- -181: Stacktrace: -181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -181: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 12# 0x00007EFC8E8552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 14# 0x00007EFC9128B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 16# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 17# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 18# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -181: 19# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 20# 0x00007EFC8E7AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 21# 0x00007EFC8E7AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 22# 0x00007EFC8E7AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 23# 0x00007EFC8E7AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 24# 0x00007EFC8E7AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 25# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 26# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 27# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 28# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 30# 0x00007EFC912883C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 31# _PyObject_MakeTpCall in /usr/bin/python3 -181: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 33# 0x0000000000546E76 in /usr/bin/python3 -181: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 35# _PyObject_Call_Prepend in /usr/bin/python3 -181: 36# 0x000000000059D6E4 in /usr/bin/python3 -181: 37# _PyObject_MakeTpCall in /usr/bin/python3 -181: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 39# 0x0000000000546E76 in /usr/bin/python3 -181: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 41# _PyObject_Call_Prepend in /usr/bin/python3 -181: 42# 0x000000000059D6E4 in /usr/bin/python3 -181: 43# _PyObject_MakeTpCall in /usr/bin/python3 -181: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 45# 0x0000000000546E76 in /usr/bin/python3 -181: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 47# _PyObject_Call_Prepend in /usr/bin/python3 -181: 48# 0x000000000059D6E4 in /usr/bin/python3 -181: 49# _PyObject_MakeTpCall in /usr/bin/python3 -181: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 51# _PyObject_Call_Prepend in /usr/bin/python3 -181: 52# 0x000000000059810D in /usr/bin/python3 -181: 53# 0x0000000000593E22 in /usr/bin/python3 -181: 54# _PyObject_MakeTpCall in /usr/bin/python3 -181: 55# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 56# PyEval_EvalCode in /usr/bin/python3 -181: 57# 0x00000000005FFE7F in /usr/bin/python3 -181: 58# 0x00000000006A59F2 in /usr/bin/python3 -181: 59# _PyRun_SimpleFileObject in /usr/bin/python3 -181: 60# _PyRun_AnyFileObject in /usr/bin/python3 -181: 61# Py_RunMain in /usr/bin/python3 -181: 62# Py_BytesMain in /usr/bin/python3 -181: 63# 0x00007EFC91A41D68 in /lib/x86_64-linux-gnu/libc.so.6 -181: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -181: 65# _start in /usr/bin/python3 -181: ---------- -181: **** -181: -181: [09:09:00] -181: -181: **** -181: Pre-condition Violation -181: RingInfo not initialized -181: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -181: Failed Expression: df_init -181: ---------- -181: Stacktrace: -181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 3# 0x00007EFC8E2E5020 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 13# 0x00007EFC8E8552B5 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 15# 0x00007EFC9128B62C in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 17# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 18# 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-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 19# 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-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -181: 20# 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-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 21# 0x00007EFC8E7AE633 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 22# 0x00007EFC8E7AE603 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 23# 0x00007EFC8E7AE5D3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 24# 0x00007EFC8E7AE5A3 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 25# 0x00007EFC8E7AE573 in /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -181: 26# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 27# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 28# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 29# 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-x86_64-linux-gnu/rdkit/rdBase.so -181: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 31# 0x00007EFC912883C6 in /lib/x86_64-linux-gnu/libboost_python312.so.1.83.0 -181: 32# _PyObject_MakeTpCall in /usr/bin/python3 -181: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 34# 0x0000000000546E76 in /usr/bin/python3 -181: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 36# _PyObject_Call_Prepend in /usr/bin/python3 -181: 37# 0x000000000059D6E4 in /usr/bin/python3 -181: 38# _PyObject_MakeTpCall in /usr/bin/python3 -181: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 40# 0x0000000000546E76 in /usr/bin/python3 -181: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 42# _PyObject_Call_Prepend in /usr/bin/python3 -181: 43# 0x000000000059D6E4 in /usr/bin/python3 -181: 44# _PyObject_MakeTpCall in /usr/bin/python3 -181: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 46# 0x0000000000546E76 in /usr/bin/python3 -181: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 48# _PyObject_Call_Prepend in /usr/bin/python3 -181: 49# 0x000000000059D6E4 in /usr/bin/python3 -181: 50# _PyObject_MakeTpCall in /usr/bin/python3 -181: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 52# _PyObject_Call_Prepend in /usr/bin/python3 -181: 53# 0x000000000059810D in /usr/bin/python3 -181: 54# 0x0000000000593E22 in /usr/bin/python3 -181: 55# _PyObject_MakeTpCall in /usr/bin/python3 -181: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 57# PyEval_EvalCode in /usr/bin/python3 -181: 58# 0x00000000005FFE7F in /usr/bin/python3 -181: 59# 0x00000000006A59F2 in /usr/bin/python3 -181: 60# _PyRun_SimpleFileObject in /usr/bin/python3 -181: 61# _PyRun_AnyFileObject in /usr/bin/python3 -181: 62# Py_RunMain in /usr/bin/python3 -181: 63# Py_BytesMain in /usr/bin/python3 -181: 64# 0x00007EFC91A41D68 in /lib/x86_64-linux-gnu/libc.so.6 -181: 65# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -181: 66# _start in /usr/bin/python3 -181: ---------- -181: **** -181: 148: processing 148: launch :0 148: launch :1 148: launch :2 148: launch :3 -218: Randomness seeded to: 4090292774 -218: =============================================================================== -218: All tests passed (203 assertions in 1 test case) -218: -219/230 Test #218: testMolProcessing ...................... Passed 5.69 sec -146: .........[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: .[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: .[09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -146: [09:09:04] Molecule does not have explicit Hs. Consider calling AddHs() -181: ............. -181: ---------------------------------------------------------------------- -181: Ran 19 tests in 25.483s -181: -181: OK -181: Testing atom rings -181: testing bond rings -181: searching atom rings -181: searching bond rings -181: done -220/230 Test #181: pySubstructLibrary ..................... Passed 26.04 sec +206: [17:55:16] Explicit valence for atom # 0 Br, 1, is greater than permitted +206: =============================================================================== +206: All tests passed (38339 assertions in 50 test cases) +206: +221/230 Test #206: molStandardizeCatchTest ................ Passed 12.24 sec +146: .........[17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: [17:55:16] Molecule does not have explicit Hs. Consider calling AddHs() 146: ... 146: ---------------------------------------------------------------------- -146: Ran 22 tests in 47.238s +146: Ran 22 tests in 17.876s 146: 146: OK -221/230 Test #146: pyDistGeomHelpers ...................... Passed 48.25 sec -206: [09:09:10] Explicit valence for atom # 0 Br, 1, is greater than permitted -206: =============================================================================== -206: All tests passed (38339 assertions in 50 test cases) -206: -222/230 Test #206: molStandardizeCatchTest ................ Passed 22.75 sec +222/230 Test #146: pyDistGeomHelpers ...................... Passed 18.23 sec +31: [17:55:19] Finished +31: [17:55:19] ------------------------------------- +31: [17:55:19] Test github1843: RWMol.clear() should not destroy ring pointer. +31: [17:55:19] Finished +31: [17:55:19] ------------------------------------- +31: [17:55:19] Test Github 6370: non-physical radical counts being preserved +31: [17:55:19] Finished +223/230 Test #31: graphmolTest1 .......................... Passed 20.00 sec +5: [17:55:20] Finished: testMultipleTimes() +5: [17:55:20] +5: ----------------------------------------- +224/230 Test #5: testConcurrentQueue .................... Passed 20.63 sec 148: --------------------------------- 148: test getO3AForProbeConfs 148: 148: *********************************************************** -223/230 Test #148: testO3AAlign ........................... Passed 53.25 sec -145: [09:09:27] UFFTYPER: Unrecognized atom type: S_6+6 (0) -145: [09:09:27] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -145: [09:09:27] UFFTYPER: Unrecognized charge state for atom: 0 -31: [09:09:38] Finished -31: [09:09:38] ------------------------------------- -31: [09:09:38] Test github1843: RWMol.clear() should not destroy ring pointer. -31: [09:09:38] Finished -31: [09:09:38] ------------------------------------- -31: [09:09:38] Test Github 6370: non-physical radical counts being preserved -31: [09:09:38] Finished -224/230 Test #31: graphmolTest1 .......................... Passed 85.55 sec -144: [09:09:46] done -144: [09:09:46] --------------------------------- -144: [09:09:46] test github issue 256: handling of zero-atom molecules +225/230 Test #148: testO3AAlign ........................... Passed 21.07 sec +229: DbCLI/UnitTestDbCLI.py ............ [100%] +229: +229: =============================== warnings summary =============================== +229: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 +229: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) +229: decBase = declarative_base() +229: +229: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +229: ======================== 12 passed, 1 warning in 16.81s ======================== +226/230 Test #229: pythonProjectTests ..................... Passed 17.43 sec +145: [17:55:28] UFFTYPER: Unrecognized atom type: S_6+6 (0) +145: [17:55:28] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +145: [17:55:28] UFFTYPER: Unrecognized charge state for atom: 0 +144: [17:55:35] done +169: =============================================================================== +169: All tests passed (93 assertions in 5 test cases) +169: +227/230 Test #169: testRascalCluster ...................... Passed 35.71 sec +144: [17:55:35] --------------------------------- +144: [17:55:35] test github issue 256: handling of zero-atom molecules 144: -144: [09:09:46] --------------------------------- -144: [09:09:46] test embedder callback function -144: [09:09:46] --------------------------------- -144: [09:09:46] test multi-threaded multi-conf embedding +144: [17:55:35] --------------------------------- +144: [17:55:35] test embedder callback function +144: [17:55:35] --------------------------------- +144: [17:55:35] test multi-threaded multi-conf embedding 144: -144: [09:09:52] --------------------------------- -144: [09:09:52] test github issue 563: Incorrect ring stereochemistry after embedding +144: [17:55:38] --------------------------------- +144: [17:55:38] 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: -225/230 Test #169: testRascalCluster ...................... Passed 84.56 sec -144: [09:09:55] --------------------------------- -144: [09:09:55] test github issue 568: Incorrect stereochemistry after embedding +144: [17:55:39] --------------------------------- +144: [17:55:39] test github issue 568: Incorrect stereochemistry after embedding 144: 144: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 -168: =============================================================================== -168: All tests passed (2923 assertions in 27 test cases) -168: -226/230 Test #168: testRascalMCES ......................... Passed 86.66 sec 144: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 144: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 144: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 @@ -35108,18 +35154,18 @@ 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 144: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +168: =============================================================================== +168: All tests passed (2923 assertions in 27 test cases) +168: +228/230 Test #168: testRascalMCES ......................... Passed 45.07 sec 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 +144: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 145: =============================================================================== 145: All tests passed (12735 assertions in 18 test cases) 145: -227/230 Test #145: distGeomHelpersCatch ................... Passed 113.94 sec -5: [09:10:15] Finished: testMultipleTimes() -5: [09:10:15] -5: ----------------------------------------- -228/230 Test #5: testConcurrentQueue .................... Passed 122.39 sec -144: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 -144: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +229/230 Test #145: distGeomHelpersCatch ................... Passed 48.61 sec 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 144: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 @@ -35128,60 +35174,50 @@ 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-] -229: DbCLI/UnitTestDbCLI.py ............ [100%] -229: -229: =============================== warnings summary =============================== -229: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 -229: /build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) -229: decBase = declarative_base() -229: -229: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -229: =================== 12 passed, 1 warning in 92.03s (0:01:32) =================== -229/230 Test #229: pythonProjectTests ..................... Passed 94.25 sec -144: [09:10:42] Molecule does not have explicit Hs. Consider calling AddHs() -144: [09:10:30] --------------------------------- -144: [09:10:30] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -144: [09:10:30] --------------------------------- -144: [09:10:30] More ChEMBL molecules failing bounds smoothing. -144: [09:10:30] --------------------------------- -144: [09:10:30] ugly conformations can be generated for highly constrained ring systems. -144: [09:10:30] --------------------------------- -144: [09:10:30] test embed parameters structure. -144: [09:10:30] --------------------------------- -144: [09:10:30] test github 1227: Hs being used in RMSD filtering. -144: [09:10:30] --------------------------------- -144: [09:10:30] Failure to embed larger aromatic rings. -144: [09:10:34] --------------------------------- -144: [09:10:34] Deterministic with large random seeds -144: [09:10:39] --------------------------------- -144: [09:10:39] Github #1990: seg fault after RemoveHs -144: [09:10:39] --------------------------------- -144: [09:10:39] Github #2246: Use coordMap when starting embedding from random coords -144: [09:10:41] --------------------------------- -144: [09:10:41] Providing a distance bounds matrix. -144: [09:10:41] --------------------------------- -144: [09:10:41] Disabling fragmentation. -144: [09:10:41] --------------------------------- -144: [09:10:41] Using symmetry in conformation pruning. -144: [09:10:42] --------------------------------- -144: [09:10:42] Force trans amides. -144: [09:10:42] --------------------------------- -144: [09:10:42] test missing Hs warning. -144: [09:10:42] --------------------------------- -144: [09:10:42] basic H bond support. -144: [09:10:42] ******************************************************* -230/230 Test #144: testDistGeomHelpers .................... Passed 141.30 sec +144: [17:55:59] Molecule does not have explicit Hs. Consider calling AddHs() +144: [17:55:54] --------------------------------- +144: [17:55:54] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +144: [17:55:54] --------------------------------- +144: [17:55:54] More ChEMBL molecules failing bounds smoothing. +144: [17:55:54] --------------------------------- +144: [17:55:54] ugly conformations can be generated for highly constrained ring systems. +144: [17:55:54] --------------------------------- +144: [17:55:54] test embed parameters structure. +144: [17:55:55] --------------------------------- +144: [17:55:55] test github 1227: Hs being used in RMSD filtering. +144: [17:55:55] --------------------------------- +144: [17:55:55] Failure to embed larger aromatic rings. +144: [17:55:56] --------------------------------- +144: [17:55:56] Deterministic with large random seeds +144: [17:55:58] --------------------------------- +144: [17:55:58] Github #1990: seg fault after RemoveHs +144: [17:55:58] --------------------------------- +144: [17:55:58] Github #2246: Use coordMap when starting embedding from random coords +144: [17:55:59] --------------------------------- +144: [17:55:59] Providing a distance bounds matrix. +144: [17:55:59] --------------------------------- +144: [17:55:59] Disabling fragmentation. +144: [17:55:59] --------------------------------- +144: [17:55:59] Using symmetry in conformation pruning. +144: [17:55:59] --------------------------------- +144: [17:55:59] Force trans amides. +144: [17:55:59] --------------------------------- +144: [17:55:59] test missing Hs warning. +144: [17:55:59] --------------------------------- +144: [17:55:59] basic H bond support. +144: [17:55:59] ******************************************************* +230/230 Test #144: testDistGeomHelpers .................... Passed 59.22 sec 99% tests passed, 1 tests failed out of 230 -Total Test time (real) = 149.33 sec +Total Test time (real) = 60.24 sec The following tests FAILED: 230 - pythonSourceTests (Failed) Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu' -dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 returned exit code 2 +dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 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 @@ -35191,7 +35227,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202409.2' dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/rdkit-202409.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.2 -B/build/reproducible-path/rdkit-202409.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -35202,1267 +35238,1267 @@ /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/__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/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/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/chemutils.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/retest.txt --- 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/chemdraw.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/spiral.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/sping --- 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/__init__.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/pidQt.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart --- 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/Pyart/Fontmapping.py --- 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/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/colors.py --- 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/pagesizes.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-1.1.1.diff --- 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/__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/pdfgen.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/PDF/pdfdoc.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/pdfutils.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/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/testallps.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/PIL --- 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/helvetica-bold-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/symbol-8.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-18.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-8.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/symbol-10.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/times-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/symbol-12.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/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.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/helvetica-bold-12.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/courier-10.pil --- 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/symbol-24.pbm --- 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/courier-12.pbm --- 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/courier-24.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/symbol-10.pil --- 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/helvetica-bold-14.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/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.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-10.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/times-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/helvetica-bold-10.pbm --- 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/metrics.dat --- 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-bold-10.pil --- 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/helvetica-8.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-bold-12.pbm --- 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/helvetica-8.pbm --- 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/courier-24.pbm --- 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/times-10.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/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/symbol-18.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/times-bold-12.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/times-12.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/helvetica-10.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/helvetica-14.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/courier-8.pil.1 --- 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-bold-24.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-bold-8.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-bold-18.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/times-bold-14.pil --- 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-8.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/times-24.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-14.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/helvetica-14.pbm --- 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-12.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/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/pid.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/WX --- 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/WX/pidWX.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/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/README --- 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 --- 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/utils.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/psmetrics.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/__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/latin1MetricsCache.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/pytest.ini --- 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/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/__init__.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/NodeLib --- 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: 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/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/Filter.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/__init__.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/Dbase --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbConnection.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/TorsionFingerprints.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/MACCSkeys.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/ChemicalForceFields.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Graphs.py --- Installing: 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/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/SimilarityMaps.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/IPythonConsole.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/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features --- Installing: 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/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/__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/FeatMaps/FeatMapParser.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/PyMol.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/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState.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/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/Fragments.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/TemplateAlign.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/QED.py +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints +-- Installing: 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/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/SigFactory.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/Pharm2D/LazyGenerator.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/Utils.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/FunctionalGroups.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/Crippen.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/Lipinski.py +-- 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/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/__init__.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/MolSurf.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/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/Utils.py -- Installing: 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+-- 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/BulkTester.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/MolCatalog.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/PandasTools.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/Dbase +-- 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/DbInfo.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/DbConnection.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/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/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/pytest.ini +-- 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/__init__.py +-- 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/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/SimDivFilters +-- 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/SimDivFilters/SimilarityPickers.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/Cluster --- 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/ClusterUtils.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/murtagh_test.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/__init__.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/murtagh_test.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/Murtagh.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/Cluster/__init__.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/ClusterUtils.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/files.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/__init__.py -- 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/MatOps.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/__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/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/BitClusterer.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/__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/MLUtils/__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/__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/CompoundDescriptors.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/__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/SLT +-- 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/SLT/Risk.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/MatOps.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/Data --- 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/Quantize.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/FindQuantBounds.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/SplitData.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/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/Transforms.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/SplitData.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/BitClusterer.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/BitRank.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/HierarchyVis.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/BitEnsemble.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/BitUtils.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/VectCollection.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/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/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/colors.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/pidWxDc.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/pidWX.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/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/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/__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/sping/tests/pstests.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/PS +-- 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/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/__init__.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/PDF +-- 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/PDF/pdfdoc.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/pdfutils.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/pdfgen.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 +-- 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/pid.py +-- 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/__init__.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/pidQt.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/pagesizes.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/Pyart +-- 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/README +-- 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/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/courier-10.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/helvetica-bold-8.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/helvetica-18.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/helvetica-bold-8.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/helvetica-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/symbol-18.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/symbol-10.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/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-12.pil +-- 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/courier-bold-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/helvetica-8.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-14.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/times-bold-18.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/courier-12.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/helvetica-bold-12.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-8.pbm +-- 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/symbol-12.pil +-- 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/times-bold-12.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/courier-bold-14.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/symbol-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/helvetica-bold-18.pil +-- 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/courier-10.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-8.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/courier-bold-24.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/helvetica-bold-14.pil +-- 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/helvetica-14.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-12.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-24.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/times-14.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/helvetica-bold-10.pil +-- 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/courier-bold-8.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/helvetica-12.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/symbol-24.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/helvetica-24.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-8.pbm +-- 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-bold-12.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/times-bold-24.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/symbol-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/courier-bold-10.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/courier-18.pil +-- 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/helvetica-18.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/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-bold-14.pbm +-- 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/metrics.dat +-- 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-24.pbm +-- 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/utils +-- 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/cactvs.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/utils/__init__.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/chemdraw_qax.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/chemdraw.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/RDConfig.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/VLib +-- 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/NodeLib +-- 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/SmilesOutput.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/DbPickleSupplier.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/DbMolSupply.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/SmilesDupeFilter.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/Filter.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/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/__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/TestRunner.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/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/share/RDKit/Data --- 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/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/FragmentDescriptors.csv +-- 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/FunctionalGroups.txt +-- 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_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/DTDs/validate.py -- 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.chk -- 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/DTDs --- 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_Dataset.dtd --- 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/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/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/SmartsLib/patty_rules.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/BaseFeatures.fdef --- 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/NCI +-- 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_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_200.tpsa.csv +-- 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/FragmentDescriptors.csv -- 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/Pains +-- 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/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/run_tests.py -- 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/README.md --- 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/test_data/wehi_mols.csv -- 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/telex_font_license.txt +-- 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/Amadeus.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/Fonts/Telex-Regular.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/Functional_Group_Hierarchy.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/rddata.sql +-- 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/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/SmartsLib/patty_rules.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs --- 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_plain.png --- 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.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.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/Book_jp --- 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_database_cartridge_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/Backwards_incompatible_changes_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/supple_images --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- 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_33.png --- 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_38.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_19.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.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_10.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_3.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_5.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.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_51.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_16.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.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_15.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.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_12.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_27.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.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_62.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.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_22.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_28.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_18.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_49.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.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_21.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.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_40.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png --- 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/Installation_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/RDKit_cookbook_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/Supplementary_Text_jp.rst --- 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/An_overview_of_the_RDKit_jp.rst +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: 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/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/RD.css -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/Chem +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai +-- 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/FragmentCatalogs.html +-- 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/CodingStandards.md +-- 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/Docs/Code/gsocGeneralFileReader.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/images +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png -- Installing: 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/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/SGroups.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md --- Installing: /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/RD.css --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- 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/Analysis/ForceField/UFF Parameters.ods --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /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/FragmentLikeT80_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/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: 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/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/RGroupDecomposition-example-lactam.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-StereoChemTest.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/Notebooks/compounds.txt --- 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/Book +-- 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/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/Overview.md +-- 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/api-docs.rst +-- 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/GettingStartedInPython.rst --- Installing: 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/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/RDKitCB_23_im1.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/EnhancedStereoSSS_molA.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_28_im1.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/RDKitCB_21_im4.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/similarity_map_charges.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_34_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/stereo_annotation.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/RDKitCB_37_im1.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/nontetstereo_tb2.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/mol_metadata1.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/mfp2_bit872.svg --- 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/atom_highlights_1.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/atrop_example5.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/picture_10.jpg --- 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/RDKitCB_37_im0.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/atrop_representation1.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_7_im6.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_3_im0.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/mcs_example_4.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/RDKitCB_30_im0.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/Cc1ccccc1.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/RDKitCB_6_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_fp3.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/cdk2_molgrid_aligned.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_1_im0.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/RDKitCB_32_im1.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_30_im1.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_6_im2.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/RDKitCB_13_im1.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/atom_annotation_1.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/mcs_example_2.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/parastereo_2.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/RDKitCB_21_im2.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/query_bonds.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/rdk_bit1553.svg --- 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/potential_stereo_double_bond1.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_7_im5.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/mcs_example_5.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/similarity_map_rf.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_6.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/similarity_map_charges.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/RDKitCB_2_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/atom_highlights_3.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_6_im1.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/mcs_example_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/RDKitCB_8_im0.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/substruct_search_parameters1.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_29_im0.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/atrop_example1.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_23_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/RDKitCB_1_im0.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_33_im1.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/nontetstereo_oh2.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_2_im1.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_35_im0.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/RDKitCB_7_im0.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_39_im0.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/ary_group.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_oh2.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/atrop_example2.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/RDKitCB_2_im0.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/RDKitCB_34_im2.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/cdk2_mol1.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/parastereo_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/RDKitCB_13_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/similarity_map_fp2.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/EnhancedStereoSSS_molE.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/RDKitCB_1_im1.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_8_im0.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/RDKitCB_23_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/EnhancedStereoSSS_molB.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/query_atoms.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/similarity_map_crippen.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/rdk_bit1553.svg +-- 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_19_im0.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_20_im1.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/mcs_example_5.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/mfp2_bit872.svg -- 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/picture_3.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_0_im2.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_34.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.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_59.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_25.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.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_43.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_29.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/The_RDKit_Book_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/Installation_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/Backwards_incompatible_changes_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/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/terminology_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/index.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/An_overview_of_the_RDKit_jp.rst +-- 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_plain.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/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.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.lrg.png +-- 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-StereoChemTest.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/FingerprintGenerators.ipynb +-- 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-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/RGroupDecomposition-MutipleCores.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/Notebooks/MolStandardize.ipynb +-- 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/RGroupDecomposition-Tests.ipynb -- 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/M_Kossner +-- 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/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/PBF +-- 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/PBFRDKit.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/Makefile +-- 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/pbf.py +-- 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/LEF +-- 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/CreateFps.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/DistancePredict.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/mmpa --- 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/README.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/test_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/create_mmp_db.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/search_mmp_db.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/mol_transform.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/data --- 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_mmps_sym.csv --- 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_mmps_maxratio.csv -- 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_input_trans.txt --- 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_mol_trans_output.txt +-- 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_mmps_maxheavy.csv +-- 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_input_trans_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/simple.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/data/sample_db_search_trans_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_db_input_subs_smarts.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_smi_output.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_transfroms.txt --- 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_smirks_mol_trans.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_mol_trans_output.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_input_subs_smarts.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_db_search_subs_smart_output.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_mmps_maxheavy.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_search_smi_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_db_search_trans_smarts_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/test_rfrag.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/FreeWilson --- 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/requirements.txt --- 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/README.md --- 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_scaffold.mol --- 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_act.csv --- 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/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/BaseFeatures_DIP2_NoMicrospecies.fdef --- 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/fraggle --- 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/fraggle/atomcontrib.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/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_fragmentation.csv --- 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.smi --- 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/mmpa/data/sample_db_input_subs.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/indexing.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/SA_Score +-- 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/fpscores.pkl.gz +-- 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/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/Fastcluster -- 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/fp.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/README.md --- 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/clustered_parse.tsv -- 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/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/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/cdk2.smi --- 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/README --- 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/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/PBF --- 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/Makefile --- 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/PBFRDKit.cpp --- 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/pbf.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/DistancePredict.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/Fastcluster/README.md +-- 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/fp.tsv +-- 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.cpp +-- 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/Wrap +-- 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/ConformerParser/Wrap/rdConformerParser.cpp +-- 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/NP_Score -- 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/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/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/__init__.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/RxnRoleAssignment/utils.py -- 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/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/figures +-- 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/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/N15.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/AKI.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/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/data --- 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/docked_2c6e_SKE_pH74_netcharge1.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_JVE_pH74_netcharge1.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/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/crystal_aligned.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/4i23_1C9.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/ACP_renamed.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/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/3w2c_N15.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/3m11_AKI.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/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/SKE_crystal_aligned_1.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/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/6c83.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/AKI_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/lig_crystal_aligned.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/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/docked_2c6e_N15_pH74_netcharge1.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/ACP_crystal_aligned_1.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/5dt0.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/3w2c_N15.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/data/ACP_crystal_aligned_2.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/AKI_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_SKE_pH74_netcharge1.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/4uzh_JVE.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/data/5dt0.pdb +-- 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/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/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/freewilson.py +-- 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/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_act.csv +-- 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.smi +-- 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/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/ConformerParser --- 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/ConformerParser.h --- 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/CMakeLists.txt --- 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/testConformerParser.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/Wrap/rdConformerParser.cpp --- 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/ChiralPairs/README.txt +-- 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/RxnRoleAssignment +-- 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/README.txt +-- 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/glare.py +-- 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/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/fraggle +-- 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/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/cxn_tversky.py +-- 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/data +-- 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/fragmentation_tversky_out +-- 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/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/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/README.md --- 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/FilterSet_NIBR2019_wPubChemExamples.html -- 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: 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/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/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/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.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/Projects --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids --- 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/testData +-- 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/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/bzr.smi --- 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/bzr --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt --- 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.sdf +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt -- 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/__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/__pycache__/UnitTestDbCLI.cpython-312-pytest-8.3.4.pyc --- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/SearchDb.cpython-312.pyc +-- 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/CreateDb.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/SearchDb.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/__pycache__/SearchDb.cpython-312.pyc +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/UnitTestDbCLI.cpython-312-pytest-8.3.4.pyc +-- 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/.pytest_cache +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md +-- Installing: /build/reproducible-path/rdkit-202409.2/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore -- 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/create_deb_packages.sh --- 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/test.sh --- 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/patch_rdkit_docstrings -- 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/patch_rdkit_docstrings/__main__.py --- 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/create_deb_packages.sh -- 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/__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/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/test.sh +-- 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/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 @@ -36506,11 +36542,11 @@ -- 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_fwd.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/hash.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/hash_float.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.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/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 @@ -37098,11 +37134,6 @@ 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-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-312-x86_64-linux-gnu.so @@ -37145,11 +37176,16 @@ I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' dh_installsystemduser -O--buildsystem=cmake @@ -37771,46 +37807,46 @@ diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.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 errcode: it's probably a plugin +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol DirectFunctionCall1Coll: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -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 PyObject_IsTrue 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 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_ValueError 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: diversions involved - output may be incorrect + diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 +dpkg-shlibdeps: warning: diversions involved - output may be incorrect + diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged 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 PyExc_KeyError 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 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 PyExc_RuntimeError 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 PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError 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: 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: /lib64/ld-linux-x86-64.so.2 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} 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: Depends field of package rdkit-doc: 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: 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 rdkit-data: 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 postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.2-2_amd64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.2-2_all.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_amd64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.2-2_all.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_amd64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.2-2_amd64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.2-2_amd64.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.2-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.2-2_amd64.buildinfo @@ -37820,12 +37856,14 @@ 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/2227627/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2227627/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/3972870 and its subdirectories -I: Current time: Tue Dec 17 09:19:42 -12 2024 -I: pbuilder-time-stamp: 1734470382 +I: removing directory /srv/workspace/pbuilder/2227627 and its subdirectories +I: Current time: Tue Jan 20 17:59:24 +14 2026 +I: pbuilder-time-stamp: 1768881564