Diff of the two buildlogs: -- --- b1/build.log 2025-04-13 07:50:50.560190302 +0000 +++ b2/build.log 2025-04-13 08:15:12.404157286 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 16 01:47:01 -12 2026 -I: pbuilder-time-stamp: 1778939221 +I: Current time: Sun Apr 13 21:50:56 +14 2025 +I: pbuilder-time-stamp: 1744530656 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 better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2321824/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/884034/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Apr 13 07:51 /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/884034/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/884034/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=42 ' - 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=40 ' + 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='6b8af3c9a5fd4959a153adf27b6e99c1' - 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='2321824' - PS1='# ' - PS2='> ' + INVOCATION_ID=d8474c3599f8423aa5e1621cce5f798a + 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=884034 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.T8J5fQI8/pbuilderrc_SNyt --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.T8J5fQI8/b1 --logfile b1/build.log rdkit_202503.1-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.T8J5fQI8/pbuilderrc_STnU --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.T8J5fQI8/b2 --logfile b2/build.log rdkit_202503.1-2.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://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2321824/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/884034/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -571,7 +603,7 @@ Get: 365 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 367 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 420 MB in 6s (70.9 MB/s) +Fetched 420 MB in 7s (63.1 MB/s) Preconfiguring packages ... 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 ... 19840 files and directories currently installed.) @@ -1750,8 +1782,8 @@ Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat May 16 13:49:17 UTC 2026. -Universal Time is now: Sat May 16 13:49:17 UTC 2026. +Local time is now: Sun Apr 13 07:52:48 UTC 2025. +Universal Time is now: Sun Apr 13 07:52:48 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.2) ... @@ -2134,7 +2166,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && 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_202503.1-2_source.changes +I: user script /srv/workspace/pbuilder/884034/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/884034/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && 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_202503.1-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-2 dpkg-buildpackage: info: source distribution unstable @@ -2258,8 +2294,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (4.5s) --- Generating done (2.0s) +-- Configuring done (8.9s) +-- Generating done (4.5s) CMake Warning: Manually-specified variables were not used by the project: @@ -2320,14 +2356,14 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.3s) +-- Configuring done (1.6s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2338,19 +2374,19 @@ 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202503.1/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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/RingFamilies /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/GA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA/CMakeFiles/ga.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/rdkitCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2360,70 +2396,70 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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 -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202503.1/External/INCHI-API/python/inchi.py /build/reproducible-path/rdkit-202503.1/rdkit/Chem/inchi.py -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build make -f 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-Dhc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-202503.1/Code/ML/Cluster/Murtagh/hc.c +[ 0%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/RandomUtil.cpp -[ 2%] Built target inchi_support +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/IntegerStringChromosomePolicy.cpp +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/External/GA/util/Util.cpp +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.cpp +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/RDGeneral/versions.cpp [ 2%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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.1.2025.03.1 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 @@ -2432,17 +2468,17 @@ [ 2%] Built target hc [ 2%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2025.03.1 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/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-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2025.03.1 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 2%] Built target ga /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-202503.1/obj-x86_64-linux-gnu' [ 2%] Built target rdkitCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 2%] Built target ga [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2025.03.1 CMakeFiles/RDStreams.dir/streams.cpp.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 @@ -2460,17 +2496,17 @@ make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" @@ -2479,15 +2515,15 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/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 make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Query /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2497,120 +2533,118 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o +[ 3%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o +[ 4%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_SIMDIVPICKERS_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 -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/FPBReader.cpp +cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/catch_logs.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/testMatrices.cpp +[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o 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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 -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-202503.1/Code/Catalogs/CatalogEntry.cpp +cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_SIMDIVPICKERS_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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/RealValueVect.cpp -[ 7%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/testMatrices.cpp -[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.cpp -[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_SIMDIVPICKERS_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 -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 +[ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMatCalc.dir/link.d CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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]: 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 7%] Linking CXX executable logTestsCatch +[ 7%] Built target EigenSolvers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target SimDivPickers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +[ 7%] Built target testConcurrentQueue make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" @@ -2619,61 +2653,70 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/SimDivPickers/testPickers.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 7%] Built target logTestsCatch [ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -[ 7%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target Catalogs +[ 7%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 7%] Built target logTestsCatch +[ 7%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 7%] Built target testMatrices [ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +[ 8%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +[ 8%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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 CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSimDivPickers.dir/link.d CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 8%] Built target testSimDivPickers +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 8%] Built target dictTestsCatch [ 8%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" 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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2681,45 +2724,33 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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 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object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-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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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testFPB.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform2D.cpp +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/pickersTestsCatch.dir/catch_tests.cpp.o -MF 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformGrid3D.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.cpp -[ 9%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -[ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/point.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testDatastructs.cpp -[ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformGrid3D.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.cpp -[ 10%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 10%] Built target testSimDivPickers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +[ 12%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 12%] Linking CXX executable pickersTestsCatch +[ 12%] Built target pickersTestsCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/InfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2025.03.1 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so [ 12%] Built target RDGeometryLib -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" -make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" +make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Features /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/CMakeFiles/testBaseFeatures.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +[ 12%] Built target InfoTheory make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake "--color=" make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 12%] Building CXX object Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -[ 12%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testRealValueGrid.cpp -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/QueryAtom.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ALIGNMENT_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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-Werror=format-security -fcf-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/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Atom.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testRealValueGrid.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/catch_tests.cpp +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend cd /build/reproducible-path/rdkit-202503.1/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 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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 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/FreeChemicalFeature.cpp -[ 14%] Building CXX object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Features/testFeatures.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Features/testFeatures.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp +[ 17%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_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 -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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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-202503.1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Aromaticity.cpp -[ 17%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -cd 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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-202503.1/obj-x86_64-linux-gnu' -[ 17%] Built target testTransforms -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ConjugHybrid.cpp [ 17%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 17%] Linking CXX executable testRealValueGrid -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRealValueGrid.dir/link.txt --verbose=1 +[ 17%] Built target rdMetricMatrixCalc +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o [ 17%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/testChemicalFeatures.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 17%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testGrid.dir/link.d CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 17%] Built target rdMetricMatrixCalc -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AddHs.cpp +[ 17%] Built target testGrid +[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ConjugHybrid.cpp [ 18%] Linking CXX executable geometryTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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testTransforms [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolProps.cpp.o -MF CMakeFiles/GraphMol.dir/MolProps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolProps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProps.cpp [ 20%] Linking CXX executable testDataStructs cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 20%] Built target rdAlignment +[ 20%] Built target rdInfoTheory [ 20%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 @@ -3144,27 +3180,27 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" @@ -3177,124 +3213,124 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 20%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -[ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o [ 20%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -[ 20%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o +[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +[ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o [ 20%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o [ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -[ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Node.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 20%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +[ 21%] Building CXX object 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +[ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Writer.cpp +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +[ 22%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/lex.yysmiles.cpp.o -MF 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-Wformat -Werror=format-security -fcf-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/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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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Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o @@ -3307,36 +3343,10 @@ cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule3.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule4c.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 [ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -[ 24%] Linking CXX executable tableTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 24%] Linking CXX executable tableTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 24%] Built target PartialCharges +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend 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object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/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 -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2025.03.1 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleBend.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversion.cpp cd /build/reproducible-path/rdkit-202503.1/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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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/ForceField/UFF/Params.cpp cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/TorsionAngle.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Nonbonded.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 26%] Built target CIPLabeler +[ 27%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 +[ 27%] Built target CIPLabeler make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 27%] Built target GenericGroups -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend -make[4]: 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd 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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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3497,56 +3517,56 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 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Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o [ 27%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_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 -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202503.1/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/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 27%] Built target testOptimizer -[ 27%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +[ 27%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp +cd /build/reproducible-path/rdkit-202503.1/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 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../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 28%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 [ 28%] Built target rdPartialCharges -[ 28%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 28%] Built target ForceField -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 -[ 28%] Built target rdCIPLabeler +[ 28%] Built target SLNParse +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 28%] Built target rdqueries +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 28%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp [ 29%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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 @@ -3566,37 +3586,58 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 29%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/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 -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 30%] Built target rdCIPLabeler +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 30%] Built target rdMolCatalog +[ 30%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 30%] Built target ForceField +[ 30%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 30%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd 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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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Built target MolInterchange +[ 30%] Built target MolInterchange make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 29%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +[ 30%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_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 -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 29%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 30%] Built target rdMolCatalog -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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-202503.1/obj-x86_64-linux-gnu' -[ 30%] Built target rdBase [ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 30%] Built target rdSLNParse +[ 30%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 [ 31%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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-202503.1/obj-x86_64-linux-gnu' +[ 31%] Built target rdBase +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 31%] Built target rdMolTransforms /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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/SmilesJSONParsers.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.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3605,26 +3646,26 @@ make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" @@ -3636,66 +3677,66 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/test2.cpp -cd /build/reproducible-path/rdkit-202503.1/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 -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -MF CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o.d -o CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_molbundle.cpp +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_queries.cpp +[ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/test1.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs/catch_tests.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 32%] Built target rdMolTransforms [ 32%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +[ 32%] Built target rdShapeHelpers /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3709,12 +3750,12 @@ make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" @@ -3726,10 +3767,10 @@ make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3737,190 +3778,185 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +[ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +[ 33%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp -cd /build/reproducible-path/rdkit-202503.1/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 -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/querytest.cpp -[ 33%] Building CXX 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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/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 34%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.cpp -[ 36%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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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-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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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 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 @@ -3935,21 +3971,27 @@ make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make 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Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ 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CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/test1.cpp -[ 39%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +[ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so [ 39%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +[ 39%] Built target FragCatalog /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3962,96 +4004,102 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 39%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/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 -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 39%] Built target FragCatalog [ 39%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -[ 39%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 39%] Built target MolAlign -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" +[ 39%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 [ 39%] Built target ForceFieldHelpers -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build -cd 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 40%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/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 -DIN_MAEPARSER -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 -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 40%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 40%] Built target testReducedGraphs +[ 40%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 [ 40%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +[ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202503.1/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 40%] Built target graphmolqueryTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 40%] Built target MolChemicalFeatures make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend @@ -4061,35 +4109,28 @@ make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make 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-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd 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CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 40%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +cd 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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 -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-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp [ 40%] Built target rdReducedGraphs -[ 40%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +[ 40%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 40%] Built target testSLNParse make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 [ 40%] 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-202503.1/obj-x86_64-linux-gnu' @@ -4098,9 +4139,11 @@ 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-202503.1/obj-x86_64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 41%] Linking CXX executable ForceFieldsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4108,26 +4151,19 @@ make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp [ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -[ 41%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Linking CXX executable ForceFieldsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 -[ 41%] Built target testSLNParse /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 41%] Built target ForceFieldsCatch @@ -4141,39 +4177,37 @@ 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 make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp cd /build/reproducible-path/rdkit-202503.1/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 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-Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 41%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdMolChemicalFeatures +[ 41%] Built target smaTest1 [ 41%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 -[ 41%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4186,79 +4220,81 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/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 -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 41%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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-202503.1/obj-x86_64-linux-gnu' +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +[ 41%] Built target rdCoordGen +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target smaTest1 -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdAbbreviations [ 41%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +[ 41%] Built target rdForceFieldHelpers +[ 41%] Built target rdMolChemicalFeatures /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 41%] Built target testDistGeom -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdForceFieldHelpers -[ 41%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 [ 41%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script 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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-202503.1/obj-x86_64-linux-gnu' -[ 41%] Built target rdCoordGen /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2025.03.1 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 41%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && 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Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o +[ 42%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +[ 42%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/INCHI-API/inchi.cpp +cd /build/reproducible-path/rdkit-202503.1/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 -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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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 -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-202503.1/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp cd /build/reproducible-path/rdkit-202503.1/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 -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolFragmenterJSONParser.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenterJSONParser.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ 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Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/hashfunctions.cpp [ 42%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +[ 42%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_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 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' @@ -4271,44 +4307,39 @@ [ 42%] Built target DistGeomHelpers [ 42%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd 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CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target MolHash +[ 42%] Built target MolHash make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 42%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/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 -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target rdMHFPFingerprint -[ 43%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so +[ 42%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2025.03.1 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target RDInchiLib +[ 42%] Built target RDInchiLib make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o +[ 42%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/External/INCHI-API/Wrap/pyInchi.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 43%] Built target rdMHFPFingerprint [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -[ 43%] Built target rdFingerprintGenerator /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 43%] Built target rdDepictor @@ -4317,6 +4348,11 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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-202503.1/obj-x86_64-linux-gnu' [ 43%] Built target rdMIF +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 43%] Built target rdFingerprintGenerator [ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 @@ -4324,82 +4360,82 @@ [ 43%] Built target rdMolHash [ 43%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 +[ 44%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 43%] Built target ChemTransforms +[ 44%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/CDXMLParser.cpp -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/Mol2FileParser.cpp cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileParser.cpp -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/Mol2FileParser.cpp cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupParsing.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MolFileWriter.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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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/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesWriter.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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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/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTWriter.cpp cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SVGParser.cpp -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp -[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 47%] Built target rdinchi [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 @@ -4416,32 +4452,32 @@ make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/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 directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" @@ -4449,324 +4485,315 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" -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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" +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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/testUFFForceField.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" -[ 50%] Linking CXX executable testSquiggleDoubleBonds +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/testSequence.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 51%] Linking CXX executable testSquiggleDoubleBonds +[ 51%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 +[ 51%] Built target testMol2ToMol +make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/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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Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=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 /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 51%] Built target testTplParser +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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4775,56 +4802,57 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-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.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 51%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 -[ 51%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 51%] Built target testAtropisomers +[ 52%] Built target testAtropisomers 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" +[ 52%] Built target graphmolOrganometallicsCatch make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 52%] Built target testTplParser -[ 52%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 52%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp +[ 53%] Built target molopsTestsCatch +make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 52%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable graphmolOrganometallicsCatch -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 53%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +[ 53%] Linking CXX executable resMolSupplierTest +[ 53%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 53%] Built target graphmoltestPicklerGlobalSetting 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" -[ 53%] Built target molopsTestsCatch -[ 53%] Built target resMolSupplierTest -make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PNGParser.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp [ 53%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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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 -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.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target graphmolOrganometallicsCatch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 53%] Built target resMolSupplierTest +make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend +[ 53%] Built target nontetrahedralCatch +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/atropisomersCatch.dir/atropisomers_catch.cpp.o -MF CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o.d -o CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/atropisomers_catch.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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 @@ -4876,74 +4910,79 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 53%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 53%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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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-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target testUFFForceField 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +[ 53%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 [ 53%] Building CXX object 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 54%] Built target graphmolSGroupCatch -[ 54%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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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/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-202503.1/Code/GraphMol/Fingerprints/test1.cpp -[ 54%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -[ 54%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202503.1/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 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 55%] Built target XYZFileParserCatchTest -[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp +[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 55%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR2D.cpp [ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 56%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 56%] Built target testSGroup -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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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 -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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 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../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 56%] Built target testMolWriter +[ 56%] Built target testSGroup make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" @@ -5094,399 +5102,369 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 56%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -[ 56%] Linking CXX executable molfileStereoCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.cpp -[ 56%] Linking CXX executable v2MolSuppliers -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 56%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.cpp -[ 57%] Built target molfileStereoCatchTest make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" +[ 56%] Built target testMolWriter make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MORSE.cpp -[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/GETAWAY.cpp +[ 57%] Built target testMMFFForceField make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 59%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.cpp -[ 59%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +[ 57%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends 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Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 59%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202503.1/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-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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/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 +[ 57%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +[ 57%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 59%] Built target testMolSupplier -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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 57%] Built target filterCatalogTest +[ 57%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ 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CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -[ 62%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -[ 62%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 62%] Built target testChemTransforms +[ 60%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +[ 60%] Built target ChemReactions make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory 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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/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 63%] Built target chemTransformsTestCatch -[ 63%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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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/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +[ 61%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 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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-202503.1/obj-x86_64-linux-gnu' -[ 63%] Built target testShapeHelpers -[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_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 -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp +cd /build/reproducible-path/rdkit-202503.1/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 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molAlignCatchTest -[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_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 -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp +[ 63%] Built target chemTransformsTestCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202503.1/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-202503.1/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:515:28, - 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-202503.1/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))); - | ^ -[ 67%] Linking CXX executable testFingerprintGenerators 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 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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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rdmolops.cpp -[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MolOps.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 63%] Built target testMolCatalog +[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_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 -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 63%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o -MF CMakeFiles/testMIF.dir/testMIF.cpp.o.d -o CMakeFiles/testMIF.dir/testMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/testMIF.cpp -[ 69%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /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/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 71%] Built target trajectoryTest -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory 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Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Normalize.cpp -[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && 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../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 71%] Built target molHashCatchTest +[ 69%] Built target MMPA 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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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-202503.1/obj-x86_64-linux-gnu' +[ 71%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +[ 71%] Built target molInterchangeCatchTest +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 72%] Built target testAbbreviations +[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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testMMPA +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 74%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +[ 74%] Built target rdMMPA +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2025.03.1 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so +[ 74%] Linking CXX executable testMolProcessing +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 73%] Built target FMCS +[ 74%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +[ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 73%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 73%] Built target MolProcessing +[ 74%] Built target testMolProcessing make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +[ 75%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 74%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -[ 74%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -[ 74%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make 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-O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FMCS/Test/testFMCS.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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-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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 74%] Built target molInterchangeTest1 -make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -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-202503.1/obj-x86_64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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target fileParsersCatchTest -[ 75%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 75%] Built target molInterchangeCatchTest -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -[ 75%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 75%] Built target testReactionFingerprints -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp -[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -[ 76%] Linking CXX executable deprotectTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend -[ 76%] Linking CXX executable testAbbreviations +[ 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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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d 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make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target testAbbreviations -[ 77%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -[ 77%] Linking CXX executable testMIF -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMIF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 77%] Built target fileParsersTest1 +[ 77%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202503.1/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-202503.1/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:515:28, + 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-202503.1/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target testEnumeration [ 77%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +[ 77%] Built target rdMolEnumerator cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMIF.dir/link.d CMakeFiles/testMIF.dir/testMIF.cpp.o -o testMIF ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target testMIF /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/DCLV.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -5944,739 +6035,677 @@ 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 80%] Building CXX object 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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/descriptorsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/catch_tests.cpp -cd /build/reproducible-path/rdkit-202503.1/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 -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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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build -make[4]: Entering directory 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-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.1.2025.03.1 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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 80%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build make[4]: Leaving directory 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/usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 80%] Built target FMCStest +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 80%] Built target graphmolMolOpsTest +[ 80%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 80%] Built target testRascalCluster /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 80%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -[ 83%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 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../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target testCoulombMat -[ 83%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target graphmolMolOpsTest -[ 83%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 83%] Built target testRDFcustom -[ 83%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 84%] Built target test3D -[ 84%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +[ 82%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Validate.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 84%] Built target MarvinParser +[ 82%] Built target MarvinParser make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend -make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse 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../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 82%] Built target testATF +make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler 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Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 86%] Linking CXX executable molFragmentTest +[ 87%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +[ 87%] Built target testRDFcustom +[ 87%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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+[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +[ 87%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +[ 87%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +[ 88%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 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../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so -[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MaeWriter.cpp -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/SDMolSupplier.cpp +[ 88%] Built target TautomerQuery make -f 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Conformer.cpp [ 89%] Built target ScaffoldNetwork [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +[ 89%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o [ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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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-202503.1/Code/GraphMol/MolDraw2D/rxn_test1.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -[ 89%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem 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/build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupData.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 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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-202503.1/obj-x86_64-linux-gnu' -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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Chirality.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/TDTWriter.cpp -[ 89%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, @@ -6705,13 +6734,6 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 -[ 89%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 89%] Built target testO3AAlign 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-202503.1/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] @@ -6731,24 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/PDBWriter.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -[ 89%] Linking CXX executable molStandardizeCatchTest +[ 90%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 90%] Built target molStandardizeCatchTest +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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +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-202503.1/obj-x86_64-linux-gnu' +[ 90%] Building CXX object 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 90%] Built target moldraw2DRxnTest1 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -6757,81 +6813,57 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 90%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 91%] Built target cxsmilesTest -[ 91%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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-g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target rdMolStandardize -[ 92%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 92%] Built target rdMolAlign +[ 92%] Linking CXX executable testCIPLabeler +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target moldraw2DTest1 +[ 92%] Built target testCIPLabeler [ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +[ 92%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 92%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so [ 92%] Built target rdMolDescriptors +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 92%] Built target rdMolStandardize +[ 92%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 -[ 92%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/GeneralizedSubstruct.dir/link.d 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CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o 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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 92%] Built target GeneralizedSubstruct make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend 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 Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend +make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" -make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -[ 93%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -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_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -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_SYNTHONSPACESEARCH_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 -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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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-202503.1/Code/PgSQL/rdkit/mol_op.c -cd /build/reproducible-path/rdkit-202503.1/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=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-202503.1/Code/PgSQL/rdkit/rdkit_gist.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && 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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/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp [ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-202503.1/Code/PgSQL/rdkit/bfp_gist.c -[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc 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{ | ~~~~~~~~~~~~~^~~~~~~~ -[ 95%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o 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-Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompJSONParsers.cpp.o ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 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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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target RGroupDecomposition +[ 97%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make 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CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target rdScaffoldNetwork -[ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.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 +[ 97%] Built target rdchem +[ 97%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 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../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 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target rdChemReactions [ 97%] Linking CXX executable generalizedSubstructCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 +[ 97%] Built target rdGeneralizedSubstruct /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +[ 97%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdChemReactions +[ 97%] Built target gaExample +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target testRGroupDecompInternals [ 97%] Linking CXX shared library librdkit.so +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql -[ 97%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/data +[ 97%] Built target rdMolDraw2D cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target rdkit -[ 97%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target testReaction -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target testRGroupDecompInternals -[ 97%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitga.so.1.2025.03.1 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../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 97%] Built target rdchem +[ 97%] Built target rdRGroupDecomposition +[ 97%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 [ 97%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rgroupCatchTests /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o 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../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 [ 97%] Built target SynthonSpaceSearch make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -7047,6 +7091,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/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 -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp +[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -7055,91 +7101,81 @@ make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build -[ 97%] Linking CXX executable rgroupCatchTests make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +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 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -MF 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/catch_tests.cpp cd /build/reproducible-path/rdkit-202503.1/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 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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-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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rgroupCatchTests -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 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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-202503.1/obj-x86_64-linux-gnu' -[ 98%] Built target moldraw2DTestCatch +[ 98%] Built target testRGroupDecomp +[ 98%] Linking CXX executable substructLibraryCatchTest [ 98%] Linking CXX executable testSynthonSpaceRascalSearch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 98%] Built target testSynthonSpaceRascalSearch -[ 98%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 98%] Built target testSynthonSpaceRascalSearch [ 98%] Built target substructLibraryCatchTest [ 99%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target substructLibraryTest -[ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target testRGroupDecomp [ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 99%] Built target rdSynthonSpaceSearch [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': ./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:334:(.text+0x1866): warning: the use of `tmpnam' is dangerous, better use `mkstemp' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target rdSynthonSpaceSearch +[ 99%] Linking CXX executable moldraw2DTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 99%] Built target moldraw2DTestCatch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 @@ -7271,77 +7307,77 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory 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files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/data +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers @@ -7351,12 +7387,12 @@ Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures @@ -8379,6 +8415,11 @@ Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... 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... @@ -8391,22 +8432,17 @@ Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... +Generating code for file Inversion.h... +Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... -Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... -Generating code for file StretchBend.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 Inversion.h... -Generating code for file Inversions.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... @@ -8506,8 +8542,6 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -8564,11 +8598,11 @@ Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... +Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... -Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... @@ -8627,6 +8661,8 @@ Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MIFDescriptors.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... @@ -8829,6 +8865,11 @@ Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... 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... @@ -8841,22 +8882,17 @@ Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... +Generating docs for file Inversion.h... +Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... -Generating docs for file OopBend.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... -Generating docs for file StretchBend.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 Inversion.h... -Generating docs for file Inversions.h... Generating docs for file Utils.h... Generating docs for file Utils.h... Generating docs for file Grid3D.h... @@ -8956,8 +8992,6 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -9014,11 +9048,11 @@ Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... +Generating docs for file MMFF.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... -Generating docs for file MMFF.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... @@ -9050,11 +9084,11 @@ Generating docs for file DrawShape.h... Generating docs for file DrawText.h... Generating docs for file DrawTextCairo.h... -Generating docs for file DrawTextFT./build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' -h... +Generating docs for file DrawTextFT.h... Generating docs for file DrawTextFTCairo.h... -Generating docs for file DrawTextFTJS.h... +Generating docs for file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' +DrawTextFTJS.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... @@ -9079,6 +9113,8 @@ Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... Generating docs for file MIFDescriptors.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... @@ -11249,9 +11285,9 @@ copying downloadable files... [100%] C++Examples/example16.cpp copying static files... -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... @@ -12537,10 +12573,10 @@ done preparing documents... done copying assets... -copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc +copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkrc -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc done copying assets: done processing RDKit.tex... @@ -12808,7 +12844,7 @@ resolving references... /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] -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 @@ -14936,10 +14972,10 @@ find /build/reproducible-path/rdkit-202503.1 -name rdchem.so /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -15193,18 +15229,6 @@ 40: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -test 41 - Start 41: graphmolMemTest1 - -41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: resMolSupplierTest - -42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15662,401 +15686,41 @@ 1: 2 5 1 0 1: M END 1: -1: cyclosporine a -1: RDKit 2D -1: -1: 85 85 0 0 0 0 0 0 0 0999 V2000 -1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 3 2 1 1 -1: 3 4 1 0 -1: 4 5 2 0 -1: 4 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 8 10 1 0 -1: 10 11 1 0 -1: 11 12 1 0 -1: 12 13 2 0 -1: 12 14 1 0 -1: 14 15 1 0 -1: 15 16 1 0 -1: 16 17 2 0 -1: 16 18 1 0 -1: 18 19 1 0 -1: 19 20 1 0 -1: 20 21 2 0 -1: 20 22 1 0 -1: 22 23 1 0 -1: 23 24 1 0 -1: 24 25 2 0 -1: 24 26 1 0 -1: 26 27 1 0 -1: 27 28 1 0 -1: 28 29 2 0 -1: 28 30 1 0 -1: 30 31 1 0 -1: 31 32 1 0 -1: 32 33 2 0 -1: 32 34 1 0 -1: 34 35 1 0 -1: 35 36 1 0 -1: 36 37 2 0 -1: 36 38 1 0 -1: 38 39 1 0 -1: 39 40 1 0 -1: 40 41 2 0 -1: 40 42 1 0 -1: 43 42 1 6 -1: 43 44 1 0 -1: 44 45 2 0 -1: 44 46 1 0 -1: 43 47 1 0 -1: 47 48 1 0 -1: 48 49 1 6 -1: 48 50 1 0 -1: 50 51 1 0 -1: 51 52 2 0 -1: 52 53 1 0 -1: 47 54 1 1 -1: 42 55 1 0 -1: 39 56 1 6 -1: 56 57 1 0 -1: 56 58 1 0 -1: 38 59 1 0 -1: 35 60 1 6 -1: 60 61 1 0 -1: 61 62 1 0 -1: 61 63 1 0 -1: 34 64 1 0 -1: 31 65 1 6 -1: 65 66 1 0 -1: 66 67 1 0 -1: 66 68 1 0 -1: 30 69 1 0 -1: 27 70 1 6 -1: 23 71 1 6 -1: 19 72 1 6 -1: 72 73 1 0 -1: 73 74 1 0 -1: 73 75 1 0 -1: 18 76 1 0 -1: 15 77 1 6 -1: 77 78 1 0 -1: 77 79 1 0 -1: 11 80 1 6 -1: 80 81 1 0 -1: 81 82 1 0 -1: 81 83 1 0 -1: 10 84 1 0 -1: 6 85 1 0 -1: 46 3 1 0 -1: M END -1: -1: single-double -1: RDKit 2D -1: -1: 17 16 0 0 0 0 0 0 0 0999 V2000 -1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 2 3 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 9 10 1 0 -1: 10 11 2 3 -1: 11 12 1 0 -1: 12 13 2 3 -1: 13 14 1 0 -1: 14 15 2 3 -1: 15 16 1 0 -1: 16 17 1 0 -1: M END -1: -1: cis-trans -1: RDKit 2D -1: -1: 10 9 0 0 0 0 0 0 0 0999 V2000 -1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 2 0 -1: 3 4 1 0 -1: 4 5 2 0 -1: 5 6 1 0 -1: 6 7 2 0 -1: 7 8 1 0 -1: 8 9 2 0 -1: 9 10 1 0 -1: M END -1: -1: admntn -1: RDKit 2D -1: -1: 10 12 0 0 0 0 0 0 0 0999 V2000 -1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 5 6 1 0 -1: 6 7 1 0 -1: 7 8 1 0 -1: 8 9 1 0 -1: 6 10 1 0 -1: 8 1 1 0 -1: 9 4 1 0 -1: 10 2 1 0 -1: M END -1: -1: github 4845 - nan coordinates but no crash -1: RDKit 2D -1: -1: 42 44 0 0 0 0 0 0 0 0999 V2000 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 2 4 2 0 -1: 4 5 1 0 -1: 5 6 3 0 -1: 6 7 1 0 -1: 7 8 2 0 -1: 8 9 1 0 -1: 9 10 3 0 -1: 10 11 1 0 -1: 11 12 2 0 -1: 12 13 1 0 -1: 13 14 3 0 -1: 14 15 1 0 -1: 15 16 2 0 -1: 16 17 1 0 -1: 16 18 1 0 -1: 12 19 1 0 -1: 19 20 2 0 -1: 20 21 1 0 -1: 20 22 1 0 -1: 19 23 1 0 -1: 23 24 3 0 -1: 24 25 1 0 -1: 25 26 1 0 -1: 26 27 2 0 -1: 27 28 2 0 -1: 26 29 1 0 -1: 29 30 3 0 -1: 8 31 1 0 -1: 31 32 2 0 -1: 32 33 1 0 -1: 32 34 1 0 -1: 31 35 1 0 -1: 35 36 3 0 -1: 36 37 1 0 -1: 37 38 2 0 -1: 37 39 1 0 -1: 39 40 2 0 -1: 40 41 1 0 -1: 40 42 1 0 -1: 39 4 1 0 -1: 15 7 1 0 -1: 30 11 1 0 -1: M END -1: -3: [02:03:55] Testing Github940: property dictionaries leaking memory -3: [02:03:55] done +3: [22:06:10] Testing Github940: property dictionaries leaking memory +3: [22:06:10] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000432 s -3: dynamic boost any:0.001695 s -3: static RDAny:0.000229 s -3: dynamic RDAny:0.001615 s +3: static boost any:0.000446 s +3: dynamic boost any:0.001718 s +3: static RDAny:0.00026 s +3: dynamic RDAny:0.001721 s 3: static RDValue:1e-06 s -3: dynamic RDValue:0.000314 s +3: dynamic RDValue:0.000325 s 3: deleted! -3: [02:03:55] ------------------------------------- -3: [02:03:55] Testing String Pickle Roundtrips. -3: [02:03:55] done -3: [02:03:55] ------------------------------------- -3: [02:03:55] Testing conversion of vect to string. -3: [02:03:55] done -3: [02:03:55] ------------------------------------- -3: [02:03:55] Testing returning const references. -3: [02:03:55] any cast -3: [02:03:55] done: 0.001286 300000 -3: [02:03:55] copy -3: [02:03:55] done: 0.00124 300000 -3: [02:03:55] ref -3: [02:03:55] done: 0.001349 300000 -3: [02:03:55] dict -3: [02:03:55] done: 0.003276 300000 -3: [02:03:55] ref with hasVal -3: [02:03:55] done: 0.002185 300000 -3: [02:03:55] done -3: [02:03:55] ------------------------------------- -3: [02:03:55] Testing dict update. -3: [02:03:55] done +3: [22:06:10] ------------------------------------- +3: [22:06:10] Testing String Pickle Roundtrips. +3: [22:06:10] done +3: [22:06:10] ------------------------------------- +3: [22:06:10] Testing conversion of vect to string. +3: [22:06:10] done +3: [22:06:10] ------------------------------------- +3: [22:06:10] Testing returning const references. +3: [22:06:10] any cast +3: [22:06:10] done: 0.001364 300000 +3: [22:06:10] copy +3: [22:06:10] done: 0.001388 300000 +3: [22:06:10] ref +3: [22:06:10] done: 0.001372 300000 +3: [22:06:10] dict +3: [22:06:10] done: 0.002657 300000 +3: [22:06:10] ref with hasVal +3: [22:06:10] done: 0.00209 300000 +3: [22:06:10] done +3: [22:06:10] ------------------------------------- +3: [22:06:10] Testing dict update. +3: [22:06:10] done 3: deleted! 3: deleted! 3: deleted! @@ -16075,48 +15739,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [02:03:55] +5: [22:06:10] 5: ----------------------------------------- -5: [02:03:55] Finished: testPushAndPop() -5: [02:03:55] +5: [22:06:10] Finished: testPushAndPop() +5: [22:06:10] 5: ----------------------------------------- -5: [02:03:55] +5: [22:06:10] 5: ----------------------------------------- -6: Randomness seeded to: 2956523307 +6: Randomness seeded to: 1159995298 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: Randomness seeded to: 1574508949 -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent -7: [02:03:55] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: Randomness seeded to: 2130233932 +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent +7: [22:06:10] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [02:03:55] pass -8: [02:03:55] v3 4 -8: [02:03:55] v4 5 -8: [02:03:55] SPARSE ----------------------------------- -8: [02:03:55] Set 10: 0 -8: [02:03:55] Set 11: 0 -8: [02:03:55] Set 14: 0 -8: [02:03:55] Set 10: 1 -8: [02:03:55] Get 14: 1 -8: [02:03:55] Num: 20 -8: [02:03:55] NumOn: 3 -8: [02:03:55] NumOff: 17 +8: [22:06:10] pass +8: [22:06:10] v3 4 +8: [22:06:10] v4 5 +8: [22:06:10] SPARSE ----------------------------------- +8: [22:06:10] Set 10: 0 +8: [22:06:10] Set 11: 0 +8: [22:06:10] Set 14: 0 +8: [22:06:10] Set 10: 1 +8: [22:06:10] Get 14: 1 +8: [22:06:10] Num: 20 +8: [22:06:10] NumOn: 3 +8: [22:06:10] NumOff: 17 8: 10, 11, 14, -8: [02:03:55] t2[19]: 0 -8: [02:03:55] t2[14]: 1 -8: [02:03:55] t2[19]: 0 -8: [02:03:55] t2[14]: 0 +8: [22:06:10] t2[19]: 0 +8: [22:06:10] t2[14]: 1 +8: [22:06:10] t2[19]: 0 +8: [22:06:10] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16124,20 +15788,20 @@ 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: [02:03:55] Explicit ---------------------------------- -8: [02:03:55] Set 10: 0 -8: [02:03:55] Set 11: 0 -8: [02:03:55] Set 14: 0 -8: [02:03:55] Set 10: 1 -8: [02:03:55] Get 14: 1 -8: [02:03:55] Num: 20 -8: [02:03:55] NumOn: 3 -8: [02:03:55] NumOff: 17 +8: [22:06:10] Explicit ---------------------------------- +8: [22:06:10] Set 10: 0 +8: [22:06:10] Set 11: 0 +8: [22:06:10] Set 14: 0 +8: [22:06:10] Set 10: 1 +8: [22:06:10] Get 14: 1 +8: [22:06:10] Num: 20 +8: [22:06:10] NumOn: 3 +8: [22:06:10] NumOff: 17 8: 10, 11, 14, -8: [02:03:55] t2[19]: 0 -8: [02:03:55] t2[14]: 1 -8: [02:03:55] t2[19]: 0 -8: [02:03:55] t2[14]: 0 +8: [22:06:10] t2[19]: 0 +8: [22:06:10] t2[14]: 1 +8: [22:06:10] t2[19]: 0 +8: [22:06:10] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16145,34 +15809,34 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [02:03:55] Done -8: [02:03:55] Test DiscreteValue Vectors 1 ---------------------------- -8: [02:03:55] Expected failure: Value out of range -8: [02:03:55] Expected failure: Value out of range -8: [02:03:55] Expected failure: Value out of range -8: [02:03:55] Expected failure: Value out of range -8: [02:03:55] Expected failure: Value out of range -8: [02:03:55] Test DiscreteValue Vectors 2 ------------------------------ -8: [02:03:55] Test DiscreteValue Vectors 3 --------------------------- -8: [02:03:55] Test DiscreteValue Operations ----------------------------- -8: [02:03:55] Test DiscreteValue Operations 2 -------------------------- -8: [02:03:55] Test SparseIntVect ------------------------------------ -8: [02:03:55] Test SparseIntVect Serialization -------------------------- -8: [02:03:55] Test BitVect Serialization ------------------------------- -8: [02:03:55] Test BitVect to FPS ------------------------------- -8: [02:03:55] Test BitVect to binary string ------------------------------- -8: [02:03:55] Test Similarity Measures BitVect ------------------------------- -8: [02:03:55] Test Similarity Measures SparseBitVect ------------------------------- -8: [02:03:55] Test BitVect with all ones ------------------------------- -8: [02:03:55] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [02:03:55] Test bitmap operations ------------------------------- -8: [02:03:55] Test bitmaps as properties ------------------------------- -8: [02:03:55] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [02:03:55] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [02:03:55] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [02:03:55] Test RealValue Vectors 3: Pickles ------------------------------- -8: [02:03:55] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 4261157611 +8: [22:06:10] Done +8: [22:06:10] Test DiscreteValue Vectors 1 ---------------------------- +8: [22:06:10] Expected failure: Value out of range +8: [22:06:10] Expected failure: Value out of range +8: [22:06:10] Expected failure: Value out of range +8: [22:06:10] Expected failure: Value out of range +8: [22:06:10] Expected failure: Value out of range +8: [22:06:10] Test DiscreteValue Vectors 2 ------------------------------ +8: [22:06:10] Test DiscreteValue Vectors 3 --------------------------- +8: [22:06:10] Test DiscreteValue Operations ----------------------------- +8: [22:06:10] Test DiscreteValue Operations 2 -------------------------- +8: [22:06:10] Test SparseIntVect ------------------------------------ +8: [22:06:10] Test SparseIntVect Serialization -------------------------- +8: [22:06:10] Test BitVect Serialization ------------------------------- +8: [22:06:10] Test BitVect to FPS ------------------------------- +8: [22:06:10] Test BitVect to binary string ------------------------------- +8: [22:06:10] Test Similarity Measures BitVect ------------------------------- +8: [22:06:10] Test Similarity Measures SparseBitVect ------------------------------- +8: [22:06:10] Test BitVect with all ones ------------------------------- +8: [22:06:10] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [22:06:10] Test bitmap operations ------------------------------- +8: [22:06:10] Test bitmaps as properties ------------------------------- +8: [22:06:10] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [22:06:10] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [22:06:10] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [22:06:10] Test RealValue Vectors 3: Pickles ------------------------------- +8: [22:06:10] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 3204026005 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -16184,8 +15848,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 1.90403 1.41147 ref2: 1.93277 2.83305 -17: pt1: 2.52997 4.69462 pt2: 1.90707 1.90822 +17: ref1: 3.71607 1.7622 ref2: 0.270105 4.60596 +17: pt1: 3.70441 1.86802 pt2: 2.03181 2.83487 17: **************************************** 17: test23D 17: **************************************** @@ -16231,24 +15895,20 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: -20: Randomness seeded to: 1099319976 +20: Randomness seeded to: 1737923753 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: -22: [02:03:57] ----------------------------------------- -22: [02:03:57] Testing RDNumerics: vectors and matrices Code -22: [02:03:57] --------------------------------------- -22: [02:03:57] test1Vector -22: [02:03:57] --------------------------------------- -22: [02:03:57] test2Matrix -22: [02:03:57] --------------------------------------- -22: [02:03:57] test3SquareMatrix -22: [02:03:57] --------------------------------------- -22: [02:03:57] test4SymmMatrix -23: Randomness seeded to: 4074321186 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: +22: [22:06:10] ----------------------------------------- +22: [22:06:10] Testing RDNumerics: vectors and matrices Code +22: [22:06:10] --------------------------------------- +22: [22:06:10] test1Vector +22: [22:06:10] --------------------------------------- +22: [22:06:10] test2Matrix +22: [22:06:10] --------------------------------------- +22: [22:06:10] test3SquareMatrix +22: [22:06:10] --------------------------------------- +22: [22:06:10] test4SymmMatrix 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- @@ -16266,82 +15926,33 @@ 26: ------------------------------------- 26: Testing BFGS optimization. 26: done -27: Randomness seeded to: 3569912887 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: -28: ------------------------------------- -28: Unit tests for force field basics. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF angle terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF angle-bend terms. -28: theta = 3.14159; theta0 = 3.14159 -28: theta = 2.094395, param1.theta0 = 2.094395 -28: done -28: ------------------------------------- -28: Test Simple UFF molecule optimizations. -28: done -28: ------------------------------------- -28: Unit tests for UFF nonbonded terms. -28: done -28: ------------------------------------- -28: Test UFF torsional terms. -28: done -28: ------------------------------------- -28: Test UFF Parameter objects -28: ------------------------------------- -28: Test Simple UFF molecule optimization, part 2. -28: done -28: ------------------------------------- -28: Test UFF Torsion Conflicts. -28: C 0.4783 -0.7477 -0.0753 -28: C -0.5465 -0.0176 0.3519 -28: C -0.5114 1.4472 0.0870 -28: H -1.5201 -0.4838 0.2485 -28: H 0.4696 1.8363 0.3367 -28: O -1.2618 1.9423 0.6934 -28: F -0.7163 1.6298 -0.9622 -28: done -28: ------------------------------------- -28: Unit tests for UFF distance constraint terms. -28: done -28: ------------------------------------- -28: Unit tests for all UFF constraint terms. -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. -29: ------------------------------------- -29: Official MMFF validation suite. - 1/236 Test #1: testCoordGen ........................... Passed 2.28 sec - 2/236 Test #3: testDict ............................... Passed 2.34 sec - 3/236 Test #4: testRDValue ............................ Passed 2.33 sec - 4/236 Test #6: dictTestsCatch ......................... Passed 2.33 sec - 5/236 Test #7: logTestsCatch .......................... Passed 2.33 sec - 6/236 Test #8: testDataStructs ........................ Passed 2.32 sec - 7/236 Test #9: testFPB ................................ Passed 2.32 sec - 8/236 Test #10: testMultiFPB ........................... Passed 2.32 sec - 9/236 Test #11: catchDataStructs ....................... Passed 2.32 sec - 10/236 Test #17: testTransforms ......................... Passed 2.30 sec - 11/236 Test #18: testGrid ............................... Passed 2.30 sec - 12/236 Test #19: testRealValueGrid ...................... Passed 2.30 sec - 13/236 Test #20: geometryTestsCatch ..................... Passed 2.30 sec - 14/236 Test #22: testMatrices ........................... Passed 2.29 sec - 15/236 Test #23: testConrec ............................. Passed 0.14 sec - 16/236 Test #24: testAlignment .......................... Passed 0.14 sec - 17/236 Test #26: testOptimizer .......................... Passed 0.14 sec - 18/236 Test #27: ForceFieldsCatch ....................... Passed 0.14 sec + 1/236 Test #3: testDict ............................... Passed 0.08 sec + 2/236 Test #4: testRDValue ............................ Passed 0.08 sec + 3/236 Test #6: dictTestsCatch ......................... Passed 0.08 sec + 4/236 Test #7: logTestsCatch .......................... Passed 0.08 sec + 5/236 Test #8: testDataStructs ........................ Passed 0.07 sec + 6/236 Test #9: testFPB ................................ Passed 0.07 sec + 7/236 Test #10: testMultiFPB ........................... Passed 0.07 sec + 8/236 Test #11: catchDataStructs ....................... Passed 0.07 sec + 9/236 Test #17: testTransforms ......................... Passed 0.06 sec + 10/236 Test #18: testGrid ............................... Passed 0.05 sec + 11/236 Test #19: testRealValueGrid ...................... Passed 0.05 sec + 12/236 Test #20: geometryTestsCatch ..................... Passed 0.05 sec + 13/236 Test #22: testMatrices ........................... Passed 0.04 sec + 14/236 Test #24: testAlignment .......................... Passed 0.04 sec + 15/236 Test #26: testOptimizer .......................... Passed 0.04 sec +test 41 + Start 41: graphmolMemTest1 + +41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +test 42 + Start 42: resMolSupplierTest + +42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 test 43 Start 43: molBundleTest @@ -16420,6 +16031,139 @@ 55: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 +31: *********************************************************** +31: test1 +31: *********************************************************** +31: testIssue216 +31: Rows: 4 Columns: 4 +31: 0 1 1 1 +31: 1 0 1 1 +31: 1 1 0 1 +31: 1 1 1 0 +31: *********************************************************** +31: + 16/236 Test #31: testDistGeom ........................... Passed 0.10 sec +29: ------------------------------------- +29: Official MMFF validation suite. +28: ------------------------------------- +28: Unit tests for force field basics. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF angle terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF angle-bend terms. +28: theta = 3.14159; theta0 = 3.14159 +28: theta = 2.094395, param1.theta0 = 2.094395 +28: done +28: ------------------------------------- +28: Test Simple UFF molecule optimizations. +28: done +28: ------------------------------------- +28: Unit tests for UFF nonbonded terms. +28: done +28: ------------------------------------- +28: Test UFF torsional terms. +28: done +28: ------------------------------------- +28: Test UFF Parameter objects +28: ------------------------------------- +28: Test Simple UFF molecule optimization, part 2. +28: done +28: ------------------------------------- +28: Test UFF Torsion Conflicts. +28: C 0.4783 -0.7477 -0.0753 +28: C -0.5465 -0.0176 0.3519 +28: C -0.5114 1.4472 0.0870 +28: H -1.5201 -0.4838 0.2485 +28: H 0.4696 1.8363 0.3367 +28: O -1.2618 1.9423 0.6934 +28: F -0.7163 1.6298 -0.9622 +28: done +28: ------------------------------------- +28: Unit tests for UFF distance constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for all UFF constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. +33: +33: +33: +33: COPY + 17/236 Test #33: graphmolcpTest ......................... Passed 0.10 sec +23: Randomness seeded to: 2358691611 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: + 18/236 Test #23: testConrec ............................. Passed 0.12 sec +27: Randomness seeded to: 372777398 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: + 19/236 Test #27: ForceFieldsCatch ....................... Passed 0.11 sec +34: [22:06:10] ---------------------- Test1 +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test2 +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test3 +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test4 +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test5 +34: [22:06:10] Done! +34: [22:06:10] +34: +34: **** +34: Pre-condition Violation +34: Can't expand empty query +34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp +34: Failed Expression: dp_query +34: ---------- +34: Stacktrace: +34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +34: 3# 0x000055D708C737EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x000055D708C710AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x00007FF39C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +34: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +34: 7# 0x000055D708C71121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: ---------- +34: **** +34: +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test issue 2892580 +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test github issue 53: query molecules not matching [R] +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test queries using qualifiers instead of == +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test extra atom queries +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test extra bond queries +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test num heteroatom neighbor queries +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test atom type queries +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [22:06:10] Done! +34: [22:06:10] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [22:06:10] Done! + 20/236 Test #34: graphmolqueryTest ...................... Passed 0.10 sec test 56 Start 56: tableTestsCatch @@ -16450,91 +16194,30 @@ 60: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -33: -33: -33: -33: COPY - 19/236 Test #33: graphmolcpTest ......................... Passed 0.17 sec -31: *********************************************************** -31: test1 -31: *********************************************************** -31: testIssue216 -31: Rows: 4 Columns: 4 -31: 0 1 1 1 -31: 1 0 1 1 -31: 1 1 0 1 -31: 1 1 1 0 -31: *********************************************************** -31: - 20/236 Test #31: testDistGeom ........................... Passed 0.30 sec -34: [02:03:57] ---------------------- Test1 -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test2 -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test3 -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test4 -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test5 -34: [02:03:57] Done! -34: [02:03:57] -34: -34: **** -34: Pre-condition Violation -34: Can't expand empty query -34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp -34: Failed Expression: dp_query -34: ---------- -34: Stacktrace: -34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -34: 3# 0x000055878FE497EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x000055878FE470AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x00007FCFA2033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -34: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -34: 7# 0x000055878FE47121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: ---------- -34: **** -34: -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test issue 2892580 -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test github issue 53: query molecules not matching [R] -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test queries using qualifiers instead of == -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test extra atom queries -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test extra bond queries -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test num heteroatom neighbor queries -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test atom type queries -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [02:03:57] Done! -34: [02:03:57] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [02:03:57] Done! - 21/236 Test #34: graphmolqueryTest ...................... Passed 0.28 sec +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing String Pickle Roundtrips. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing reading existing pickle file (v2). +38: [22:06:10] done +40: [22:06:10] Testing the hanoi sort +40: [22:06:10] populating vectors 35: 1 1 2 35: 1 1 1 35: 2 1 0.75 35: path: 2 -35: [02:03:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [02:03:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [02:03:57] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [02:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [02:03:57] Explicit valence for atom # 1 Si, 7, is greater than permitted +35: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [22:06:10] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [22:06:10] Explicit valence for atom # 1 Si, 7, is greater than permitted 35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -35: [02:03:57] non-ring atom 0 marked aromatic -35: [02:03:57] non-ring atom 0 marked aromatic -35: [02:03:57] Conflicting single bond directions around double bond at index 17. -35: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [22:06:10] non-ring atom 0 marked aromatic +35: [22:06:10] non-ring atom 0 marked aromatic +35: [22:06:10] Conflicting single bond directions around double bond at index 17. +35: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. 35: starting ring finding 35: done 35: starting ring finding @@ -16543,6 +16226,1009 @@ 35: done 35: 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 35: starting sanitization +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +36: [22:06:10] Conflicting single bond directions around double bond at index 2. +36: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [22:06:10] Conflicting single bond directions around double bond at index 4. +36: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [22:06:10] Conflicting single bond directions around double bond at index 15. +36: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [22:06:10] Conflicting single bond directions around double bond at index 2. +36: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [22:06:10] Conflicting single bond directions around double bond at index 1. +36: [22:06:10] BondStereo set to STEREONONE and single bond directions set to NONE. +36: -------------------------------------------------- +46: Randomness seeded to: 3641983352 +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [22:06:10] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [22:06:10] non-ring atom 2 marked aromatic +46: [22:06:10] non-ring atom 2 marked aromatic +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [22:06:10] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [22:06:10] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [22:06:10] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [22:06:10] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [22:06:10] WARNING: not removing hydrogen atom with wedged bond +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] Unreasonable formal charge on atom # 0. +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E96F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E999D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no atom +46: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: at +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1EA2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: no owner +46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h +46: Failed Expression: dp_mol +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9B08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: atom not associated with this molecule +46: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: &at->getOwningMol() == this +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9BA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: null atom passed in +46: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: atom_pin +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1EA291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: cannot take ownership of an atom which already has an owner +46: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1E9EB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: cannot take ownership of an bond which already has an owner +46: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp +46: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1EA26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: not removing hydrogen atom without neighbors +46: [22:06:10] Explicit valence for atom # 1 F greater than permitted +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: plain atoms have no Query +46: Violation occurred on line 697 in file ./Code/GraphMol/Atom.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE19114B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: plain atoms have no Query +46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE1911E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: plain bonds have no Query +46: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE190E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] +46: +46: **** +46: Pre-condition Violation +46: plain bonds have no query +46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp +46: Failed Expression: 0 +46: ---------- +46: Stacktrace: +46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +46: 3# 0x000055A3BE190F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x000055A3BE236938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x000055A3BE237458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x000055A3BE2378D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x000055A3BE208F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x000055A3BE2092AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x000055A3BE183DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007F1ACAC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +46: 12# 0x000055A3BE183E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: ---------- +46: **** +46: +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: Randomness seeded to: 1818596810 +47: =============================================================================== +47: All tests passed (62 assertions in 6 test cases) +47: +48: Randomness seeded to: 555496774 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: +50: Randomness seeded to: 830889111 +50: [22:06:10] unable to set wavy bonds for double bonds: 3 +50: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 21/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.11 sec + 22/236 Test #39: graphmolIterTest ....................... Passed 0.11 sec + 23/236 Test #41: graphmolMemTest1 ....................... Passed 0.09 sec + 24/236 Test #43: molBundleTest .......................... Passed 0.09 sec + 25/236 Test #44: testSGroup ............................. Passed 0.09 sec + 26/236 Test #45: test-valgrind .......................... Passed 0.09 sec + 27/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.08 sec + 28/236 Test #48: graphmolSGroupCatch .................... Passed 0.08 sec +test 61 + Start 61: smaTest1 + +61: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +61: Test timeout computed to be: 1500 +test 62 + Start 62: smiTestCatch + +62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +62: Test timeout computed to be: 1500 +test 63 + Start 63: nontetrahedralCatch + +63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +test 64 + Start 64: v2smiTestCatch + +64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +64: Test timeout computed to be: 1500 +test 65 + Start 65: testDepictor + +65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +test 66 + Start 66: depictorCatch + +66: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +66: Test timeout computed to be: 1500 +test 67 + Start 67: pyDepictor + +67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" +67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +67: Test timeout computed to be: 1500 +test 68 + Start 68: testMrvToMol + +68: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse +68: Test timeout computed to be: 1500 + 29/236 Test #36: graphmoltestChirality .................. Passed 0.14 sec +46: [22:06:10] Unusual charge on atom 0 number of radical electrons set to zero +46: [22:06:10] Unusual charge on atom 0 number of radical electrons set to zero +46: [22:06:10] Unusual charge on atom 0 number of radical electrons set to zero +46: [22:06:10] non-ring atom 0 marked aromatic +46: [22:06:10] non-ring atom 0 marked aromatic +46: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [22:06:10] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [22:06:10] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 7 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 3 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [22:06:10] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +1: cyclosporine a +1: RDKit 2D +1: +1: 85 85 0 0 0 0 0 0 0 0999 V2000 +1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4912 -3.8491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.1202 1.6015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.1628 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.6786 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 3 2 1 1 +1: 3 4 1 0 +1: 4 5 2 0 +1: 4 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 8 10 1 0 +1: 10 11 1 0 +1: 11 12 1 0 +1: 12 13 2 0 +1: 12 14 1 0 +1: 14 15 1 0 +1: 15 16 1 0 +1: 16 17 2 0 +1: 16 18 1 0 +1: 18 19 1 0 +1: 19 20 1 0 +1: 20 21 2 0 +1: 20 22 1 0 +1: 22 23 1 0 +1: 23 24 1 0 +1: 24 25 2 0 +1: 24 26 1 0 +1: 26 27 1 0 +1: 27 28 1 0 +1: 28 29 2 0 +1: 28 30 1 0 +1: 30 31 1 0 +1: 31 32 1 0 +1: 32 33 2 0 +1: 32 34 1 0 +1: 34 35 1 0 +1: 35 36 1 0 +1: 36 37 2 0 +1: 36 38 1 0 +1: 38 39 1 0 +1: 39 40 1 0 +1: 40 41 2 0 +1: 40 42 1 0 +1: 43 42 1 6 +1: 43 44 1 0 +1: 44 45 2 0 +1: 44 46 1 0 +1: 43 47 1 0 +1: 47 48 1 0 +1: 48 49 1 6 +1: 48 50 1 0 +1: 50 51 1 0 +1: 51 52 2 0 +1: 52 53 1 0 +1: 47 54 1 1 +1: 42 55 1 0 +1: 39 56 1 6 +1: 56 57 1 0 +1: 56 58 1 0 +1: 38 59 1 0 +1: 35 60 1 6 +1: 60 61 1 0 +1: 61 62 1 0 +1: 61 63 1 0 +1: 34 64 1 0 +1: 31 65 1 6 +1: 65 66 1 0 +1: 66 67 1 0 +1: 66 68 1 0 +1: 30 69 1 0 +1: 27 70 1 6 +1: 23 71 1 6 +1: 19 72 1 6 +1: 72 73 1 0 +1: 73 74 1 0 +1: 73 75 1 0 +1: 18 76 1 0 +1: 15 77 1 6 +1: 77 78 1 0 +1: 77 79 1 0 +1: 11 80 1 6 +1: 80 81 1 0 +1: 81 82 1 0 +1: 81 83 1 0 +1: 10 84 1 0 +1: 6 85 1 0 +1: 46 3 1 0 +1: M END +1: +1: single-double +1: RDKit 2D +1: +1: 17 16 0 0 0 0 0 0 0 0999 V2000 +1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 2 3 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 9 10 1 0 +1: 10 11 2 3 +1: 11 12 1 0 +1: 12 13 2 3 +1: 13 14 1 0 +1: 14 15 2 3 +1: 15 16 1 0 +1: 16 17 1 0 +1: M END +1: +1: cis-trans +1: RDKit 2D +1: +1: 10 9 0 0 0 0 0 0 0 0999 V2000 +1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 2 0 +1: 3 4 1 0 +1: 4 5 2 0 +1: 5 6 1 0 +1: 6 7 2 0 +1: 7 8 1 0 +1: 8 9 2 0 +1: 9 10 1 0 +1: M END +1: +1: admntn +1: RDKit 2D +1: +1: 10 12 0 0 0 0 0 0 0 0999 V2000 +1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 5 6 1 0 +1: 6 7 1 0 +1: 7 8 1 0 +1: 8 9 1 0 +1: 6 10 1 0 +1: 8 1 1 0 +1: 9 4 1 0 +1: 10 2 1 0 +1: M END +1: +1: github 4845 - nan coordinates but no crash +1: RDKit 2D +1: +1: 42 44 0 0 0 0 0 0 0 0999 V2000 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: -nan -nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 2 4 2 0 +1: 4 5 1 0 +1: 5 6 3 0 +1: 6 7 1 0 +1: 7 8 2 0 +1: 8 9 1 0 +1: 9 10 3 0 +1: 10 11 1 0 +1: 11 12 2 0 +1: 12 13 1 0 +1: 13 14 3 0 +1: 14 15 1 0 +1: 15 16 2 0 +1: 16 17 1 0 +1: 16 18 1 0 +1: 12 19 1 0 +1: 19 20 2 0 +1: 20 21 1 0 +1: 20 22 1 0 +1: 19 23 1 0 +1: 23 24 3 0 +1: 24 25 1 0 +1: 25 26 1 0 +1: 26 27 2 0 +1: 27 28 2 0 +1: 26 29 1 0 +1: 29 30 3 0 +1: 8 31 1 0 +1: 31 32 2 0 +1: 32 33 1 0 +1: 32 34 1 0 +1: 31 35 1 0 +1: 35 36 3 0 +1: 36 37 1 0 +1: 37 38 2 0 +1: 37 39 1 0 +1: 39 40 2 0 +1: 40 41 1 0 +1: 40 42 1 0 +1: 39 4 1 0 +1: 15 7 1 0 +1: 30 11 1 0 +1: M END +1: +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.008s +15: +15: OK +49: Randomness seeded to: 2194897292 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: + 30/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.11 sec +52: Randomness seeded to: 1627499097 +52: =============================================================================== +52: All tests passed (14 assertions in 4 test cases) +52: + 31/236 Test #52: moliteratorTestsCatch .................. Passed 0.06 sec +53: Randomness seeded to: 3048150134 +53: =============================================================================== +53: All tests passed (10 assertions in 1 test case) +53: + 32/236 Test #53: queryTestsCatch ........................ Passed 0.06 sec +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.003s +13: +13: OK +54: Randomness seeded to: 213569249 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: + 33/236 Test #54: molbundleTestsCatch .................... Passed 0.06 sec +test 69 + Start 69: fileParsersTest1 + +69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +test 70 + Start 70: testAtropisomers + +70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +test 71 + Start 71: testSquiggleDoubleBonds + +71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +test 72 + Start 72: testMolSupplier + +72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +test 73 + Start 73: testGeneralFileReader + +73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 + 34/236 Test #1: testCoordGen ........................... Passed 0.27 sec +50: [22:06:10] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [22:06:10] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [22:06:10] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 35/236 Test #50: chiralityTestsCatch .................... Passed 0.17 sec +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.006s +16: +16: OK +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.001s +14: +14: OK + 36/236 Test #14: pyRealValueVect ........................ Passed 0.26 sec +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [22:06:10] SMILES Parse Error: syntax error while parsing: - +59: [22:06:10] SMILES Parse Error: check for mistakes around position 1: +59: [22:06:10] - +59: [22:06:10] ^ +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [22:06:10] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 37/236 Test #59: smiTest2 ............................... Passed 0.11 sec 35: done 35: starting sanitization 35: done @@ -16551,42 +17237,32 @@ 35: starting ring finding 35: done 35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [02:03:57] WARNING: not removing hydrogen atom with dummy atom neighbors +35: [22:06:10] WARNING: not removing hydrogen atom with dummy atom neighbors 35: ------------------------------- -35: [02:03:57] Explicit valence for atom # 0 N, 4, is greater than permitted -35: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [02:03:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [02:03:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:03:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:03:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:03:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [02:03:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [22:06:10] Explicit valence for atom # 0 N, 4, is greater than permitted +35: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [22:06:10] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: -35: [02:03:57] WARNING: not removing hydrogen atom with dummy atom neighbors -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -36: [02:03:57] Conflicting single bond directions around double bond at index 2. -36: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:03:57] Conflicting single bond directions around double bond at index 4. -36: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:03:57] Conflicting single bond directions around double bond at index 15. -36: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:03:57] Conflicting single bond directions around double bond at index 2. -36: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [02:03:57] Conflicting single bond directions around double bond at index 1. -36: [02:03:57] BondStereo set to STEREONONE and single bond directions set to NONE. -36: -------------------------------------------------- - 22/236 Test #36: graphmoltestChirality .................. Passed 0.28 sec -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing String Pickle Roundtrips. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing reading existing pickle file (v2). -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing combining molecules using pickles. +35: [22:06:10] WARNING: not removing hydrogen atom with dummy atom neighbors +56: Randomness seeded to: 1296609620 +56: =============================================================================== +56: All tests passed (7 assertions in 2 test cases) +56: + 38/236 Test #56: tableTestsCatch ........................ Passed 0.12 sec +55: Randomness seeded to: 2167580548 +55: =============================================================================== +55: All tests passed (45 assertions in 4 test cases) +55: + 39/236 Test #55: pickleTestsCatch ....................... Passed 0.12 sec +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing combining molecules using pickles. 37: Atoms: 37: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -16603,37 +17279,37 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Issue164: Roundtrip Pickle Failure. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Issue219: Pickle Failure with Conformations. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Issue220: Pickle problems with bond stereochemistry. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing query serialization. -37: [02:03:57] C=[$(C=O)] -37: [02:03:57] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing radical handling in pickles. -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 2788233. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 3202580. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Issue164: Roundtrip Pickle Failure. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Issue219: Pickle Failure with Conformations. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Issue220: Pickle problems with bond stereochemistry. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing query serialization. +37: [22:06:10] C=[$(C=O)] +37: [22:06:10] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing radical handling in pickles. +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 2788233. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 3316407. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 3496759. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 3316407. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16821,6 +17497,355 @@ 37: smi match: *CS *CS 37: smi match: SC(S)=C(S)S SC(S)=C(S)S 37: smi match: N=CC=NO N=CC=NO +57: Randomness seeded to: 522246536 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: + 40/236 Test #57: molopsTestsCatch ....................... Passed 0.11 sec +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.030s +2: +2: OK +64: Randomness seeded to: 1123432815 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: +test 74 + Start 74: testMultithreadedMolSupplier + +74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +test 75 + Start 75: testMolWriter + +75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +test 76 + Start 76: testTplParser + +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +test 77 + Start 77: testMol2ToMol + +77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +test 78 + Start 78: testSequence + +78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +test 79 + Start 79: testExtendedStereoParsing + +79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 +test 80 + Start 80: fileParsersCatchTest + +80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 +62: Randomness seeded to: 379867422 +62: [22:06:10] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [22:06:10] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [22:06:10] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [22:06:10] SMARTS Parse Error: syntax error while parsing: C)foo +62: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [22:06:10] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: [22:06:10] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +62: [22:06:10] w block attempts to set wedging on bond 0 more than once. +62: [22:06:10] improperly formatted w block +62: [22:06:10] atom 3 is not associated with bond 1(1-2) in w block +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] WARNING: not removing hydrogen atom without neighbors +58: [22:06:10] Invalid chiral specification on atom 0 +58: [22:06:10] Invalid chiral specification on atom 0 +58: [22:06:10] Invalid chiral specification on atom 0 +58: [22:06:10] Invalid chiral specification on atom 0 +58: [22:06:10] Invalid chiral specification on atom 0 +58: [22:06:10] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [22:06:10] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +63: Randomness seeded to: 2962613097 +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [22:06:10] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.002s +25: +25: OK +25: Testing Alignment Wrapper code: +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.001s +32: +32: OK +46: [22:06:10] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [22:06:10] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [22:06:10] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [22:06:10] non-ring atom 0 marked aromatic +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +68: [22:06:10] unsupported number of radical electrons 5 +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTest.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestNoChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: NewChiralTestAllChiral.sdf +68: +68: Test +68: +68: vendor839.sdf +68: +68: Test +68: +68: ProblemShort.mol +68: +68: [22:06:10] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: The multiple sgroup will be ignored +70: [22:06:10] ---- Running with POSIX locale ----- +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: Randomness seeded to: 1617347910 +71: =============================================================================== +71: All tests passed (15 assertions in 3 test cases) +71: +72: [22:06:10] +72: ----------------------------------------- +72: [22:06:10] Ignoring invalid chirality label: '2_bad_chirality' + 41/236 Test #13: pyDiscreteValueVect .................... Passed 0.33 sec + 42/236 Test #15: pySparseIntVect ........................ Passed 0.33 sec + 43/236 Test #16: pyFPB .................................. Passed 0.32 sec + 44/236 Test #25: pyAlignment ............................ Passed 0.30 sec + 45/236 Test #32: pyDistGeom ............................. Passed 0.29 sec + 46/236 Test #63: nontetrahedralCatch .................... Passed 0.16 sec + 47/236 Test #64: v2smiTestCatch ......................... Passed 0.16 sec + 48/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.12 sec +test 81 + Start 81: testPropertyLists + +81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +test 83 + Start 83: cdxmlParserCatchTest + +83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +test 84 + Start 84: molfileStereoCatchTest + +84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +test 85 + Start 85: connectTheDotsTest + +85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +test 86 + Start 86: v2MolSuppliers + +86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +test 87 + Start 87: v2FileParsersCatchTest + +87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 +test 88 + Start 88: atropisomersCatch + +88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch +88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 +62: [22:06:10] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 7# 0x000055944315AA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x00005594431ABD28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x00005594431AC848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x00005594431ACCC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055944317E303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055944317E66C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055944310FE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FAC43633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +62: 16# 0x000055944310FE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [22:06:10] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 7# 0x000055944315AA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x00005594431ABD28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x00005594431AC848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x00005594431ACCC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055944317E303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055944317E66C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055944310FE1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007FAC43633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +62: 16# 0x000055944310FE61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [22:06:10] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [22:06:10] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [22:06:10] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [22:06:10] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [22:06:10] SMILES Parse Error: check for mistakes around position 4: +62: [22:06:10] C1C)foo +62: [22:06:10] ~~~^ +62: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: +69: *************************************** +69: *************************************** +69: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [22:06:10] bond with order 0 found on line 7. This is not part of the MDL specification. +69: [22:06:10] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [22:06:10] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [22:06:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: generating smiles +69: 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 +69: converting back +69: check isomorphism +73: [22:06:10] +73: ----------------------------------------- +73: [22:06:10] Finished: testDetermineFormat() +73: [22:06:10] ----------------------------------------- +73: +73: [22:06:10] +73: ----------------------------------------- +73: [22:06:10] Finished: testSdf() +73: [22:06:10] ----------------------------------------- +73: +73: [22:06:10] +73: ----------------------------------------- +73: [22:06:10] Finished: testSmi() +73: [22:06:10] ----------------------------------------- +73: +73: [22:06:10] +73: ----------------------------------------- +73: [22:06:10] Finished: testMae() +73: [22:06:10] ----------------------------------------- +73: +73: [22:06:10] +73: ----------------------------------------- + 49/236 Test #2: pyCoordGen ............................. Passed 0.43 sec 37: smi match: N#CCC#N N#CCC#N 37: smi match: CON=O CON=O 37: smi match: C=CN C=CN @@ -17060,730 +18085,67 @@ 37: smi match: * * 37: smi match: ***** ***** 37: smi match: NC(N)=O NC(N)=O -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 280. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing sf.net issue 285. -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Github2441: Add RDProps interface to Conformers. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Issue2510: Pickle Confs as double. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing loading pickled mols with conformers -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing conformer reading/writing options -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing property reading options -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing property reading options -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing boost::serialization integration -37: [02:03:57] done -37: [02:03:57] ------------------------------------- -37: [02:03:57] Testing github issue 6036 -38: [02:03:57] done - 23/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.27 sec - 24/236 Test #39: graphmolIterTest ....................... Passed 0.27 sec -40: [02:03:57] Testing the hanoi sort -40: [02:03:57] populating vectors -40: [02:03:58] sorting (hanoi sort) vectors - 25/236 Test #41: graphmolMemTest1 ....................... Passed 0.27 sec -test 61 - Start 61: smaTest1 - -61: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -61: Test timeout computed to be: 1500 -test 62 - Start 62: smiTestCatch - -62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -62: Test timeout computed to be: 1500 -test 63 - Start 63: nontetrahedralCatch - -63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -test 64 - Start 64: v2smiTestCatch - -64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -test 66 - Start 66: depictorCatch - -66: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -66: Test timeout computed to be: 1500 -test 67 - Start 67: pyDepictor - -67: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap/testDepictor.py" -67: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -67: Test timeout computed to be: 1500 - 26/236 Test #37: graphmoltestPickler .................... Passed 0.29 sec -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.001s -25: -25: OK -25: Testing Alignment Wrapper code: - 27/236 Test #25: pyAlignment ............................ Passed 0.34 sec -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.008s -15: -15: OK - 28/236 Test #15: pySparseIntVect ........................ Passed 2.50 sec -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.011s -16: -16: OK - 29/236 Test #16: pyFPB .................................. Passed 2.50 sec +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 280. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing sf.net issue 285. +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Github2441: Add RDProps interface to Conformers. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Issue2510: Pickle Confs as double. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing loading pickled mols with conformers +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing conformer reading/writing options +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing property reading options +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing property reading options +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing boost::serialization integration +37: [22:06:10] done +37: [22:06:10] ------------------------------------- +37: [22:06:10] Testing github issue 6036 21: .................... 21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.060s +21: Ran 20 tests in 0.088s 21: 21: OK 21: Testing Geometry wrapper - 30/236 Test #21: testPyGeometry ......................... Passed 2.49 sec -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.003s -13: -13: OK - 31/236 Test #13: pyDiscreteValueVect .................... Passed 2.51 sec -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.002s -32: -32: OK - 32/236 Test #32: pyDistGeom ............................. Passed 0.31 sec + 50/236 Test #21: testPyGeometry ......................... Passed 0.39 sec 28: done - 33/236 Test #28: testUFFForceField ...................... Passed 0.33 sec -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.030s -2: -2: OK - 34/236 Test #2: pyCoordGen ............................. Passed 2.54 sec -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.001s -14: -14: OK - 35/236 Test #14: pyRealValueVect ........................ Passed 2.51 sec - 36/236 Test #43: molBundleTest .......................... Passed 0.20 sec - 37/236 Test #44: testSGroup ............................. Passed 0.20 sec - 38/236 Test #45: test-valgrind .......................... Passed 0.20 sec -46: Randomness seeded to: 2649728487 -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [02:03:57] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [02:03:57] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [02:03:57] non-ring atom 2 marked aromatic -46: [02:03:57] non-ring atom 2 marked aromatic -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [02:03:57] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [02:03:57] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [02:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [02:03:57] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [02:03:57] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [02:03:57] WARNING: not removing hydrogen atom with wedged bond -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] Unreasonable formal charge on atom # 0. -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9668 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F96F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 182 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9785 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 364 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9870 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9901 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 365 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F999D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no atom -46: Violation occurred on line 371 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: at -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715FA2B9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: no owner -46: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h -46: Failed Expression: dp_mol -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9B08 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: atom not associated with this molecule -46: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: &at->getOwningMol() == this -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9BA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: null atom passed in -46: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: atom_pin -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715FA291 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: cannot take ownership of an atom which already has an owner -46: Violation occurred on line 387 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715F9EB8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: cannot take ownership of an bond which already has an owner -46: Violation occurred on line 412 in file ./Code/GraphMol/ROMol.cpp -46: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715FA26D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: not removing hydrogen atom without neighbors -46: [02:03:57] Explicit valence for atom # 1 F greater than permitted -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: plain atoms have no Query -46: Violation occurred on line 697 in file ./Code/GraphMol/Atom.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715A114B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: plain atoms have no Query -46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715A11E0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: plain bonds have no Query -46: Violation occurred on line 207 in file ./Code/GraphMol/Bond.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715A0E70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] -46: -46: **** -46: Pre-condition Violation -46: plain bonds have no query -46: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp -46: Failed Expression: 0 -46: ---------- -46: Stacktrace: -46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005646715A0F05 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000564671646938 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000564671647458 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005646716478D0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000564671618F43 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005646716192AC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000564671593DDE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007F8D34E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x0000564671593E21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: ---------- -46: **** -46: -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:03:57] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:03:57] Unusual charge on atom 0 number of radical electrons set to zero -46: [02:03:57] non-ring atom 0 marked aromatic -46: [02:03:57] non-ring atom 0 marked aromatic -46: [02:03:57] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [02:03:57] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [02:03:57] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 7 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 3 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [02:03:57] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [02:03:58] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [02:03:58] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [02:03:58] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [02:03:58] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [02:03:58] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [02:03:58] non-ring atom 0 marked aromatic -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: Randomness seeded to: 2993434709 -47: =============================================================================== -47: All tests passed (62 assertions in 6 test cases) -47: - 39/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.20 sec -48: Randomness seeded to: 900831099 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: - 40/236 Test #48: graphmolSGroupCatch .................... Passed 0.20 sec -49: Randomness seeded to: 3861897276 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: - 41/236 Test #49: graphmolAdjustQueryCatch ............... Passed 0.20 sec -50: Randomness seeded to: 2179512433 -50: [02:03:57] unable to set wavy bonds for double bonds: 3 -50: [02:03:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [02:03:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [02:03:58] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [02:03:58] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [02:03:58] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -50: =============================================================================== -50: All tests passed (2295 assertions in 80 test cases) -50: - 42/236 Test #50: chiralityTestsCatch .................... Passed 0.19 sec -52: Randomness seeded to: 3913131648 -52: =============================================================================== -52: All tests passed (14 assertions in 4 test cases) -52: - 43/236 Test #52: moliteratorTestsCatch .................. Passed 0.18 sec -53: Randomness seeded to: 2027855506 -53: =============================================================================== -53: All tests passed (10 assertions in 1 test case) -53: - 44/236 Test #53: queryTestsCatch ........................ Passed 0.18 sec -54: Randomness seeded to: 3975520797 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 45/236 Test #54: molbundleTestsCatch .................... Passed 0.18 sec -55: Randomness seeded to: 410553993 -55: =============================================================================== -55: All tests passed (45 assertions in 4 test cases) -55: - 46/236 Test #55: pickleTestsCatch ....................... Passed 0.17 sec -56: Randomness seeded to: 2561385541 -56: =============================================================================== -56: All tests passed (7 assertions in 2 test cases) -56: - 47/236 Test #56: tableTestsCatch ........................ Passed 0.17 sec -57: Randomness seeded to: 3668919332 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: - 48/236 Test #57: molopsTestsCatch ....................... Passed 0.16 sec -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] WARNING: not removing hydrogen atom without neighbors -58: [02:03:57] Invalid chiral specification on atom 0 -58: [02:03:57] Invalid chiral specification on atom 0 -58: [02:03:57] Invalid chiral specification on atom 0 -58: [02:03:57] Invalid chiral specification on atom 0 -58: [02:03:57] Invalid chiral specification on atom 0 -58: [02:03:58] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [02:03:58] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [02:03:57] SMILES Parse Error: syntax error while parsing: - -59: [02:03:57] SMILES Parse Error: check for mistakes around position 1: -59: [02:03:57] - -59: [02:03:57] ^ -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [02:03:57] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [02:03:57] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 49/236 Test #59: smiTest2 ............................... Passed 0.16 sec -60: Randomness seeded to: 1380054742 + 51/236 Test #28: testUFFForceField ...................... Passed 0.38 sec +61: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [22:06:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 52/236 Test #61: smaTest1 ............................... Passed 0.25 sec +66: Randomness seeded to: 843414478 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: + 53/236 Test #66: depictorCatch .......................... Passed 0.24 sec +60: Randomness seeded to: 3076203955 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -17844,16 +18206,16 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -17862,227 +18224,23 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: Test -60: -60: JDQ443_3d.cxsmi -60: -60: Test -60: -60: JDQ443_atrop1.cxsmi -60: -60: Test -60: -60: JDQ443_atrop2.cxsmi -60: -60: Test -60: -60: JDQ443_atrop3.cxsmi -60: -60: Test -60: -60: JDQ443_atrop4.cxsmi -60: -60: Test -60: -60: JDQ443_atropBad1.cxsmi -60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: Test -60: -60: RP-6306_atrop1.cxsmi -60: -60: Test -60: -60: RP-6306_atrop2.cxsmi -60: -60: Test -60: -60: RP-6306_atrop3.cxsmi -60: -60: Test -60: -60: RP-6306_atrop4.cxsmi -60: -60: Test -60: -60: RP-6306_atrop5.cxsmi -60: -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: Test -60: -60: RP-6306_atrop6.cxsmi -60: -60: Test -60: -60: RP-6306_atropBad1.cxsmi -60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: Test -60: -60: RP-6306_atropBad2.cxsmi -60: -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -test 68 - Start 68: testMrvToMol - -68: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse -68: Test timeout computed to be: 1500 -test 69 - Start 69: fileParsersTest1 - -69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -test 70 - Start 70: testAtropisomers - -70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -test 71 - Start 71: testSquiggleDoubleBonds - -71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -test 72 - Start 72: testMolSupplier - -72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -test 73 - Start 73: testGeneralFileReader - -73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -test 74 - Start 74: testMultithreadedMolSupplier - -74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -test 75 - Start 75: testMolWriter - -75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -test 77 - Start 77: testMol2ToMol - -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -test 78 - Start 78: testSequence - -78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -test 79 - Start 79: testExtendedStereoParsing - -79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -test 80 - Start 80: fileParsersCatchTest - -80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 -test 81 - Start 81: testPropertyLists - -81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 -test 82 - Start 82: XYZFileParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -test 83 - Start 83: cdxmlParserCatchTest - -83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -test 84 - Start 84: molfileStereoCatchTest - -84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -test 85 - Start 85: connectTheDotsTest - -85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -test 86 - Start 86: v2MolSuppliers - -86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -test 87 - Start 87: v2FileParsersCatchTest - -87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -test 88 - Start 88: atropisomersCatch - -88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch -88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -88: Test timeout computed to be: 1500 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +74: [22:06:10] +74: ----------------------------------------- + 54/236 Test #76: testTplParser .......................... Passed 0.13 sec test 89 Start 89: multithreadedSupplierCatchTest @@ -18101,254 +18259,27 @@ 91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct 91: Test timeout computed to be: 1500 -58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1Br -58: smi: c1ccccc1 -58: smi: c1ccncc1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[pH]c1 -58: [02:03:58] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [02:03:58] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: CbC(aC)aC -58: CaC(bC)aC -58: CbC(bC)aC -58: O.C -58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -58: [02:03:58] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [02:03:58] SMILES Parse Error: check for mistakes around position 4: -58: [02:03:58] c%()ccccc%() -58: [02:03:58] ~~~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [02:03:58] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [02:03:58] SMILES Parse Error: check for mistakes around position 9: -58: [02:03:58] c%(100000)ccccc%(100000) -58: [02:03:58] ~~~~~~~~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [02:03:58] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [02:03:58] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [02:03:58] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMILES Parse Error: check for mistakes around position 14: -58: [02:03:58] COc(c1)cccc1C# -58: [02:03:58] ~~~~~~~~~~~~~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:03:58] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:03:58] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMILES Parse Error: check for mistakes around position 14: -58: [02:03:58] COc(c1)cccc1C# -58: [02:03:58] ~~~~~~~~~~~~~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:03:58] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:03:58] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMILES Parse Error: check for mistakes around position 14: -58: [02:03:58] COc(c1)cccc1C# -58: [02:03:58] ~~~~~~~~~~~~~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [02:03:58] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: C=c1s/c2n(c1=O)CCCCCCC\N=2 -58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -58: [02:03:58] SMILES Parse Error: extra close parentheses while parsing: C) -58: [02:03:58] SMILES Parse Error: check for mistakes around position 2: -58: [02:03:58] C) -58: [02:03:58] ~^ -58: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -30: ...[02:03:58] Molecule does not have explicit Hs. Consider calling AddHs() -62: Randomness seeded to: 1987041293 -62: [02:03:58] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [02:03:58] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [02:03:58] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [02:03:58] SMARTS Parse Error: syntax error while parsing: C)foo -62: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [02:03:58] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [02:03:58] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -62: [02:03:58] w block attempts to set wedging on bond 0 more than once. -62: [02:03:58] improperly formatted w block -62: [02:03:58] atom 3 is not associated with bond 1(1-2) in w block -63: Randomness seeded to: 583938109 -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [02:03:58] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -63: =============================================================================== -63: All tests passed (308 assertions in 9 test cases) -63: -64: Randomness seeded to: 3467725690 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 50/236 Test #64: v2smiTestCatch ......................... Passed 0.11 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 - 51/236 Test #58: smiTest1 ............................... Passed 0.25 sec - 52/236 Test #63: nontetrahedralCatch .................... Passed 0.12 sec -46: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [02:03:58] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [02:03:58] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: - 53/236 Test #46: graphmolTestsCatch ..................... Passed 0.30 sec -60: Test -60: -60: RP-6306_3d.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop1.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop2.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop3.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop4.cxsmi -60: -60: Test -60: -60: Sotorasib_atrop5.cxsmi -60: -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: Test -60: -60: Sotorasib_atropBad1.cxsmi -60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: Test -60: -60: Sotorasib_atropBad2.cxsmi -60: -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [02:03:58] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [02:03:58] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 54/236 Test #61: smaTest1 ............................... Passed 0.14 sec -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -68: [02:03:58] unsupported number of radical electrons 5 -69: *************************************** -69: *************************************** -69: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:03:58] bond with order 0 found on line 7. This is not part of the MDL specification. -69: [02:03:58] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [02:03:58] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [02:03:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: generating smiles -69: 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 -69: converting back -70: [02:03:58] ---- Running with POSIX locale ----- -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: Randomness seeded to: 4079497990 -71: =============================================================================== -71: All tests passed (15 assertions in 3 test cases) -71: - 55/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.09 sec -72: [02:03:58] -72: ----------------------------------------- -72: [02:03:58] Ignoring invalid chirality label: '2_bad_chirality' -73: [02:03:58] -73: ----------------------------------------- -73: [02:03:58] Finished: testDetermineFormat() -73: [02:03:58] ----------------------------------------- -73: -73: [02:03:58] -73: ----------------------------------------- -73: [02:03:58] Finished: testSdf() -73: [02:03:58] ----------------------------------------- -73: -73: [02:03:58] -73: ----------------------------------------- -73: [02:03:58] Finished: testSmi() -73: [02:03:58] ----------------------------------------- +test 93 + Start 93: testReaction + +93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +73: [22:06:10] Finished: testTdt() +73: [22:06:10] ----------------------------------------- 73: -73: [02:03:58] -73: ----------------------------------------- -74: [02:03:58] -74: ----------------------------------------- - 56/236 Test #76: testTplParser .......................... Passed 0.07 sec - 57/236 Test #77: testMol2ToMol .......................... Passed 0.07 sec 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -19333,28 +19264,160 @@ 78: CONECT 27 28 28 29 78: END 78: - 58/236 Test #78: testSequence ........................... Passed 0.07 sec - 59/236 Test #79: testExtendedStereoParsing .............. Passed 0.07 sec -80: Randomness seeded to: 2905592149 -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [02:03:58] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [02:03:58] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [02:03:58] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [02:03:58] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [02:03:58] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [02:03:58] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [02:03:58] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup 3 referenced on line 40 not found. -80: [02:03:58] +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1Br +58: smi: c1ccccc1 +58: smi: c1ccncc1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[pH]c1 +58: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [22:06:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: CbC(aC)aC +58: CaC(bC)aC +58: CbC(bC)aC +58: O.C +58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +58: [22:06:10] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [22:06:10] SMILES Parse Error: check for mistakes around position 4: +58: [22:06:10] c%()ccccc%() +58: [22:06:10] ~~~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [22:06:10] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [22:06:10] SMILES Parse Error: check for mistakes around position 9: +58: [22:06:10] c%(100000)ccccc%(100000) +58: [22:06:10] ~~~~~~~~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [22:06:10] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [22:06:10] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [22:06:10] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMILES Parse Error: check for mistakes around position 14: +58: [22:06:10] COc(c1)cccc1C# +58: [22:06:10] ~~~~~~~~~~~~~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [22:06:10] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [22:06:10] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMILES Parse Error: check for mistakes around position 14: +58: [22:06:10] COc(c1)cccc1C# +58: [22:06:10] ~~~~~~~~~~~~~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [22:06:10] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [22:06:10] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMILES Parse Error: check for mistakes around position 14: +58: [22:06:10] COc(c1)cccc1C# +58: [22:06:10] ~~~~~~~~~~~~~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [22:06:10] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: C=c1s/c2n(c1=O)CCCCCCC\N=2 +58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +58: [22:06:10] SMILES Parse Error: extra close parentheses while parsing: C) +58: [22:06:10] SMILES Parse Error: check for mistakes around position 2: +58: [22:06:10] C) +58: [22:06:10] ~^ +58: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [22:06:10] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [22:06:10] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +80: Randomness seeded to: 765379816 +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [22:06:10] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [22:06:10] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [22:06:10] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [22:06:10] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [22:06:10] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [22:06:10] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [22:06:10] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup 3 referenced on line 40 not found. +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19367,24 +19430,24 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x000055E0957026A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 7# 0x0000555A39C856A9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] SGroup 3 referenced on line 40 not found. -80: [02:03:58] +80: [22:06:10] SGroup 3 referenced on line 40 not found. +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19397,29 +19460,29 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x000055E095702752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 7# 0x0000555A39C85752 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] no bonds -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup line too short: 'M SBV 1 6' on line 42 -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [02:03:58] SGroup 2 is invalid and will be ignored -80: [02:03:58] +80: [22:06:10] no bonds +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup line too short: 'M SBV 1 6' on line 42 +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [22:06:10] SGroup 2 is invalid and will be ignored +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19433,23 +19496,23 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x000055E095703312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x0000555A39C86312 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19463,24 +19526,24 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x000055E0957033BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x0000555A39C863BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] +80: [22:06:10] bookmark not found +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19494,25 +19557,25 @@ 80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCDA81E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x000055E0957033BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x0000555A39C863BA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bond is not part of the SubstanceGroup -80: [02:03:58] SGroup 2 is invalid and will be ignored -80: [02:03:58] +80: [22:06:10] bond is not part of the SubstanceGroup +80: [22:06:10] SGroup 2 is invalid and will be ignored +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19526,23 +19589,23 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x000055E095703729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x0000555A39C86729 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19556,27 +19619,27 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCDA6AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x000055E0957037D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 8# 0x0000555A39C867D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [02:03:58] SGroup 2 is invalid and will be ignored -80: [02:03:58] WARNING: final character of V3000 array is not ')' -80: [02:03:58] +80: [22:06:10] bookmark not found +80: [22:06:10] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [22:06:10] SGroup 2 is invalid and will be ignored +80: [22:06:10] WARNING: final character of V3000 array is not ')' +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19594,21 +19657,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E095701033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C84033 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] WARNING: final character of V3000 array is not ')' -80: [02:03:58] +80: [22:06:10] WARNING: final character of V3000 array is not ')' +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19626,23 +19689,23 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0957010CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C840CB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] WARNING: final character of V3000 array is not ')' -80: [02:03:58] +80: [22:06:10] bookmark not found +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] WARNING: final character of V3000 array is not ')' +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19660,21 +19723,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E095701434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C84434 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] WARNING: final character of V3000 array is not ')' -80: [02:03:58] +80: [22:06:10] WARNING: final character of V3000 array is not ')' +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19692,22 +19755,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0957014CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C844CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] SGroup 1 is invalid and will be ignored -80: [02:03:58] +80: [22:06:10] bookmark not found +80: [22:06:10] SGroup 1 is invalid and will be ignored +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19725,20 +19788,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E095701833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C84833 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19756,22 +19819,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0957018CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C848CC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] SGroup 2 is invalid and will be ignored -80: [02:03:58] +80: [22:06:10] bookmark not found +80: [22:06:10] SGroup 2 is invalid and will be ignored +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19789,20 +19852,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E095701C32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C84C32 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -19820,42 +19883,165 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E095701CCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C84CCC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [22:06:10] bookmark not found +80: [22:06:10] SGroup 2 is invalid and will be ignored +80: [22:06:10] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [22:06:10] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [22:06:10] sanitize [22:06:10] UNK: [22:06:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [22:06:10] skipping block at line 7: 'BEGIN ATOM' +80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL +80: END +80: +80: [22:06:10] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp +80: Failed Expression: dp_inStream +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000555A39CB93C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000555A39C74CAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] bookmark not found -80: [02:03:58] SGroup 2 is invalid and will be ignored -80: [02:03:58] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [02:03:58] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [02:03:58] Explicit valence for atom # 1 C, 5, is greater than permitted -80: [02:03:58] sanitize [02:03:58] UNK: [02:03:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: Randomness seeded to: 302424719 +80: [22:06:10] +80: +80: **** +80: Pre-condition Violation +80: no stream +80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +80: Failed Expression: dp_inStream +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000555A39CB93C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000555A39C74E88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [22:06:10] +80: +80: **** +30: ...[22:06:10] Molecule does not have explicit Hs. Consider calling AddHs() +72: [22:06:10] Finished: testMolSup() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testRandMolSup() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSmilesSup() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ------------------------------------------------------ +72: [22:06:10] SMILES Parse Error: syntax error while parsing: fail +72: [22:06:10] SMILES Parse Error: check for mistakes around position 1: +72: [22:06:10] fail +72: [22:06:10] ^ +72: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [22:06:10] ERROR: Smiles parse error on line 3 +72: [22:06:10] ERROR: Cannot create molecule from : 'fail' +72: [22:06:10] ------------------------------------------------------ +72: [22:06:10] ------------------------------------------------------ +72: [22:06:10] >>> This may result in an infinite loop. It should finish almost immediately: +72: [22:06:10] <<< done. +72: [22:06:10] Finished: testSmilesSupFromText() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSmilesWriter() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +81: Randomness seeded to: 3247072731 81: =============================================================================== 81: All tests passed (95 assertions in 4 test cases) 81: - 60/236 Test #81: testPropertyLists ...................... Passed 0.06 sec -test 93 - Start 93: testReaction - -93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 +82: Randomness seeded to: 540684152 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: +83: Randomness seeded to: 3927761415 +83: [22:06:10] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [22:06:10] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [22:06:10] CDXMLParser: failed sanitizing skipping fragment 32 +83: [22:06:10] Bad bond in CDXML skipping fragment 58... +83: [22:06:10] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [22:06:10] Bad bond in CDXML skipping fragment 58... +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] WARNING: not removing hydrogen atom without neighbors +83: [22:06:10] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +83: [22:06:10] Incomplete atom labelling, cannot make bond +83: [22:06:10] Incomplete atom labelling, cannot make bond +84: Randomness seeded to: 4133195341 +84: [22:06:10] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [22:06:10] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [22:06:10] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [22:06:10] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: =============================================================================== +84: All tests passed (142 assertions in 6 test cases) +84: +85: Randomness seeded to: 219828678 +85: =============================================================================== +85: All tests passed (8 assertions in 1 test case) +85: + 55/236 Test #37: graphmoltestPickler .................... Passed 0.48 sec + 56/236 Test #62: smiTestCatch ........................... Passed 0.36 sec + 57/236 Test #77: testMol2ToMol .......................... Passed 0.23 sec + 58/236 Test #78: testSequence ........................... Passed 0.22 sec + 59/236 Test #79: testExtendedStereoParsing .............. Passed 0.22 sec + 60/236 Test #81: testPropertyLists ...................... Passed 0.20 sec + 61/236 Test #82: XYZFileParserCatchTest ................. Passed 0.19 sec + 62/236 Test #85: connectTheDotsTest ..................... Passed 0.15 sec test 95 Start 95: testEnumeration @@ -19904,344 +20090,24 @@ 102: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery 102: Test timeout computed to be: 1500 -60: Test -60: -60: Sotorasib_3d.cxsmi -60: -60: Test -60: -60: ZM374979_atrop1.cxsmi -60: -60: Test -60: -60: ZM374979_atrop2.cxsmi -60: -60: Test -60: -60: ZM374979_atrop3.cxsmi -60: -60: Test -60: -60: ZM374979_atrop4.cxsmi -60: -60: Test -60: -60: ZM374979_atropBad1.cxsmi -60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: check isomorphism -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -85: Randomness seeded to: 480637722 -85: =============================================================================== -85: All tests passed (8 assertions in 1 test case) -85: - 61/236 Test #85: connectTheDotsTest ..................... Passed 0.09 sec -82: Randomness seeded to: 100604892 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: - 62/236 Test #82: XYZFileParserCatchTest ................. Passed 0.11 sec -84: Randomness seeded to: 2115937802 -84: [02:03:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:03:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:03:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [02:03:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: =============================================================================== -84: All tests passed (142 assertions in 6 test cases) -84: - 63/236 Test #84: molfileStereoCatchTest ................. Passed 0.10 sec -90: ----------------- Test 1 -90: Done -90: -90: ----------------- Test 2 -90: Done -90: -90: ----------------- Test 3 -90: Done -90: -90: ----------------- Test 4 -90: Done -90: -90: ----------------- Test 5 -90: Done -90: -90: ----------------- Test 5 QueryRoot -90: Done -90: -90: ----------------- Test 6 (Issue71 related) -90: Done -90: -90: ----------------- Testing serial numbers on recursive queries -90: Done -90: -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test multithreading -90: reading molecules -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -90: launch :2 -90: launch :3 -86: Randomness seeded to: 2196281297 -86: [02:03:58] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [02:03:58] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [02:03:58] Ignoring invalid chirality label: '2_S_1_3_4' -86: [02:03:58] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: - 64/236 Test #86: v2MolSuppliers ......................... Passed 0.09 sec -87: Randomness seeded to: 3851866729 -87: =============================================================================== -87: All tests passed (6 assertions in 1 test case) -87: - 65/236 Test #87: v2FileParsersCatchTest ................. Passed 0.09 sec -66: Randomness seeded to: 1049923858 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: -88: Randomness seeded to: 864991009 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: - 66/236 Test #88: atropisomersCatch ...................... Passed 0.09 sec -62: [02:03:58] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000560284EFFA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000560284F50D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000560284F51848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000560284F51CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000560284F23303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000560284F2366C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000560284EB4E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007FE9F9233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000560284EB4E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [02:03:58] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000560284EFFA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000560284F50D28 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000560284F51848 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000560284F51CC0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000560284F23303 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000560284F2366C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000560284EB4E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007FE9F9233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000560284EB4E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [02:03:58] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [02:03:58] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [02:03:58] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [02:03:58] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [02:03:58] SMILES Parse Error: check for mistakes around position 4: -62: [02:03:58] C1C)foo -62: [02:03:58] ~~~^ -62: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -62: =============================================================================== -62: All tests passed (1588 assertions in 69 test cases) -62: -test 103 - Start 103: pyTautomerQuery - -103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 -test 104 - Start 104: testSubgraphs1 - -104: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 -test 105 - Start 105: testSubgraphs2 - -105: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -105: Test timeout computed to be: 1500 -test 106 - Start 106: subgraphsCatch - -106: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -106: Test timeout computed to be: 1500 -test 107 - Start 107: filterCatalogTest - -107: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -107: Test timeout computed to be: 1500 -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -83: Randomness seeded to: 3826630435 -83: [02:03:58] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [02:03:58] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [02:03:58] CDXMLParser: failed sanitizing skipping fragment 32 -83: [02:03:58] Bad bond in CDXML skipping fragment 58... -83: [02:03:58] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [02:03:58] Bad bond in CDXML skipping fragment 58... -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] WARNING: not removing hydrogen atom without neighbors -83: [02:03:58] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -83: [02:03:58] Incomplete atom labelling, cannot make bond -83: [02:03:58] Incomplete atom labelling, cannot make bond -83: [02:03:58] Incomplete atom labelling, cannot make bond -80: [02:03:58] skipping block at line 7: 'BEGIN ATOM' -80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL -80: END -80: -80: [02:03:58] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x000055E0957363C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x000055E0956F1CAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [02:03:58] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x000055E0957363C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x000055E0956F1E88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [02:03:58] -80: -80: **** + 63/236 Test #73: testGeneralFileReader .................. Passed 0.43 sec +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 64/236 Test #58: smiTest1 ............................... Passed 0.51 sec + 65/236 Test #46: graphmolTestsCatch ..................... Passed 0.59 sec 80: Pre-condition Violation 80: no stream 80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp @@ -20251,21 +20117,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x000055E0957363C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x000055E0956F22C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000555A39CB93C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000555A39C752C1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -20277,21 +20143,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x000055E0957363C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x000055E0956F2646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000555A39CB93C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000555A39C75646 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -20303,29 +20169,29 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x000055E0957363C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x000055E0956F28C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 3# 0x0000555A39CB93C4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000555A39C758C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [02:03:58] BEGIN SGROUP line not found on line 14 -80: [02:03:58] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [02:03:58] END SGROUP line not found on line 14 -80: [02:03:58] END SGROUP line not found on line 14 -80: [02:03:58] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [02:03:58] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [02:03:58] +80: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [22:06:10] BEGIN SGROUP line not found on line 14 +80: [22:06:10] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [22:06:10] END SGROUP line not found on line 14 +80: [22:06:10] END SGROUP line not found on line 14 +80: [22:06:10] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [22:06:10] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [22:06:10] 80: 80: **** 80: Range Error @@ -20340,38 +20206,38 @@ 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x000055E095735FDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E0956F7CC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 6# 0x0000555A39CB8FDF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39C7ACC3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [02:03:58] Multiple ATTCHPT values for atom 2 on line 9 -80: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [02:03:58] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [02:03:58] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [02:03:58] Skipping empty SMARTS value for SMARTSQ. -80: [02:03:58] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [02:03:58] WARNING: Skipping property bar because the value includes an illegal blank line -80: [02:03:58] WARNING: Skipping property baz because the value includes an illegal blank line -80: [02:03:58] WARNING: Skipping property bletch +80: [22:06:10] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [22:06:10] Multiple ATTCHPT values for atom 2 on line 9 +80: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [22:06:10] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [22:06:10] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [22:06:10] Skipping empty SMARTS value for SMARTSQ. +80: [22:06:10] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [22:06:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [22:06:10] WARNING: Skipping property bar because the value includes an illegal blank line +80: [22:06:10] WARNING: Skipping property baz because the value includes an illegal blank line +80: [22:06:10] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [02:03:58] WARNING: Skipping property bletch +80: [22:06:10] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Post-condition Violation @@ -20383,26 +20249,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F551CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007F512CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0956C935C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C4C35C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Post-condition Violation @@ -20414,26 +20280,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F551CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007F512CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCD3AC2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCD4FAD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0956C8A3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C4BA3A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Post-condition Violation @@ -20445,26 +20311,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F551CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007F512CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0956C9304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C4C304 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] +80: [22:06:10] 80: 80: **** 80: Post-condition Violation @@ -20476,28 +20342,28 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F551CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F551CCD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F551CCD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007F512CCC8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007F512CCD1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007F512CCD217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x000055E0956C8FA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x0000555A39C4BFA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [02:03:58] atom 3 has a negative isotope value. line: 15 -80: [02:03:58] Ignoring invalid chirality label: '2_bad_chirality' -80: [02:03:58] +80: [22:06:10] atom 3 has a negative isotope value. line: 15 +80: [22:06:10] Ignoring invalid chirality label: '2_bad_chirality' +80: [22:06:10] 80: 80: **** 80: Pre-condition Violation @@ -20510,310 +20376,577 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x000055E09570B7A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x000055E09577A228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x000055E09577AD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x000055E09577B1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x000055E09574C8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x000055E09574CC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x000055E0956BFC2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F551C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 4# 0x0000555A39C8E7A5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000555A39CFD228 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000555A39CFDD48 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000555A39CFE1C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000555A39CCF8C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000555A39CCFC2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000555A39C42C2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007F512C233CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x000055E0956BFC71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000555A39C42C71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTest.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestNoChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: NewChiralTestAllChiral.sdf -68: -68: Test -68: -68: vendor839.sdf -68: -68: Test -68: -68: ProblemShort.mol -68: -68: [02:03:58] For a MultipleSgroup expansion, the matching orphaned bond was not found -68: The multiple sgroup will be ignored -73: [02:03:58] Finished: testMae() -73: [02:03:58] ----------------------------------------- -73: -73: [02:03:58] -73: ----------------------------------------- -73: [02:03:58] Finished: testTdt() -73: [02:03:58] ----------------------------------------- -73: -72: [02:03:58] Finished: testMolSup() -72: [02:03:58] ----------------------------------------- +72: [22:06:10] Finished: testSDWriter() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSDSupplierEnding() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSuppliersEmptyFile() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testCisTrans() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testStereoRound() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [22:06:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [22:06:10] Finished: testIssue226() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testTDTSupplier1() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testTDTSupplier2() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testTDTSupplier3() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSDSupplierFromText() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Spurious data before the first property will be ignored +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Finished: testSDSupplierStrLax1() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Finished: testSDSupplierStrLax2() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Spurious data before the first property will be ignored +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Finished: testSDSupplierFromTextStrLax1() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: Problems encountered parsing data fields +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Property will be truncated after the first blank line +72: [22:06:10] Finished: testSDSupplierFromTextStrLax2() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testIssue265() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: End of data field name not found +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule ending on line 16 +72: [22:06:10] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [22:06:10] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] ERROR: Bond line too short: 'M END' on line 18 +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Finished: testSDErrorHandling() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testIssue381() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSetStreamIndices() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testMixIterAndRandom() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: build: +72: [22:06:10] Finished: testRemoveHs() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testGetItemText() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testForwardSDSupplier() +72: [22:06:10] ----------------------------------------- 72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testRandMolSup() -72: [02:03:58] ----------------------------------------- +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testMissingCRSDSupplier() +72: [22:06:10] ----------------------------------------- 72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSmilesSup() -72: [02:03:58] ----------------------------------------- +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testIssue3482695() +72: [22:06:10] ----------------------------------------- 72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ------------------------------------------------------ -72: [02:03:58] SMILES Parse Error: syntax error while parsing: fail -72: [02:03:58] SMILES Parse Error: check for mistakes around position 1: -72: [02:03:58] fail -72: [02:03:58] ^ -72: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [02:03:58] ERROR: Smiles parse error on line 3 -72: [02:03:58] ERROR: Cannot create molecule from : 'fail' -72: [02:03:58] ------------------------------------------------------ -72: [02:03:58] ------------------------------------------------------ -72: [02:03:58] >>> This may result in an infinite loop. It should finish almost immediately: -72: [02:03:58] <<< done. -72: [02:03:58] Finished: testSmilesSupFromText() -72: [02:03:58] ----------------------------------------- +72: [22:06:10] ----------------------------------------- +72: [22:06:10] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Finished: testIssue3525673() +72: [22:06:10] ----------------------------------------- 72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSmilesWriter() -72: [02:03:58] ----------------------------------------- +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testBlankLinesInProps() +72: [22:06:10] ----------------------------------------- 72: -72: [02:03:58] ----------------------------------------- +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testSkipLines() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testGitHub23() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testGitHub88() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +83: [22:06:10] Incomplete atom labelling, cannot make bond +83: [22:06:10] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [22:06:10] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [22:06:10] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [22:06:10] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [22:06:10] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 66/236 Test #84: molfileStereoCatchTest ................. Passed 0.30 sec +86: Randomness seeded to: 386012543 +86: [22:06:10] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [22:06:10] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [22:06:10] Ignoring invalid chirality label: '2_S_1_3_4' +86: [22:06:10] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 67/236 Test #86: v2MolSuppliers ......................... Passed 0.28 sec +88: Randomness seeded to: 3251755260 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: + 68/236 Test #88: atropisomersCatch ...................... Passed 0.26 sec +87: Randomness seeded to: 2368485143 +87: =============================================================================== +87: All tests passed (6 assertions in 1 test case) +87: + 69/236 Test #87: v2FileParsersCatchTest ................. Passed 0.27 sec +40: [22:06:10] sorting (hanoi sort) vectors +60: Test +60: +60: JDQ443_3d.cxsmi +60: +60: Test +60: +60: JDQ443_atrop1.cxsmi +60: +60: Test +60: +60: JDQ443_atrop2.cxsmi +60: +60: Test +60: +60: JDQ443_atrop3.cxsmi +60: +60: Test +60: +60: JDQ443_atrop4.cxsmi +60: +60: Test +60: +60: JDQ443_atropBad1.cxsmi +60: +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: Test +60: +60: RP-6306_atrop1.cxsmi +60: +60: Test +60: +60: RP-6306_atrop2.cxsmi +60: +60: Test +60: +60: RP-6306_atrop3.cxsmi +60: +60: Test +60: +60: RP-6306_atrop4.cxsmi +60: +60: Test +60: +60: RP-6306_atrop5.cxsmi +60: +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: Test +60: +60: RP-6306_atrop6.cxsmi +60: +60: Test +60: +60: RP-6306_atropBad1.cxsmi +60: +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: Test +60: +60: RP-6306_atropBad2.cxsmi +60: +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: Test +60: +60: RP-6306_3d.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop1.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop2.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop3.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop4.cxsmi +60: +60: Test +60: +60: Sotorasib_atrop5.cxsmi +60: +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [22:06:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: Test +60: +60: Sotorasib_atropBad1.cxsmi +60: +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: Test +60: +60: Sotorasib_atropBad2.cxsmi +60: +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [22:06:10] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +90: ----------------- Test 1 +90: Done +90: +90: ----------------- Test 2 +90: Done +90: +90: ----------------- Test 3 +90: Done +90: +90: ----------------- Test 4 +90: Done +90: +90: ----------------- Test 5 +90: Done +90: +90: ----------------- Test 5 QueryRoot +90: Done +90: +90: ----------------- Test 6 (Issue71 related) +90: Done +90: +90: ----------------- Testing serial numbers on recursive queries +90: Done +90: +90: [22:06:10] ------------------------------------- +90: [22:06:10] Test multithreading +90: reading molecules +90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing +90: launch :0 +90: launch :1 +90: launch :2 +90: launch :3 +test 103 + Start 103: pyTautomerQuery + +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 +test 104 + Start 104: testSubgraphs1 + +104: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +test 105 + Start 105: testSubgraphs2 + +105: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +105: Test timeout computed to be: 1500 +test 106 + Start 106: subgraphsCatch + +106: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +106: Test timeout computed to be: 1500 +test 107 + Start 107: filterCatalogTest + +107: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +107: Test timeout computed to be: 1500 +test 108 + Start 108: pyFilterCatalog + +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 +test 109 + Start 109: testFragCatalog + +109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 +94: [22:06:10] ------------------------------------- +94: [22:06:10] Test Reaction StructuralFingerprint +94: [22:06:10] ------------------------------------- +94: [22:06:10] Test Reaction DifferenceFingerprint 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:03:58] 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]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [22:06:10] 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]' 93: O=C1CNC(=O)CN1 -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:03:58] atom 0 in product 0 has multiple charge specifications. +93: [22:06:10] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [02:03:58] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:03:58] SMILES Parse Error: check for mistakes around position 2: -93: [02:03:58] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [02:03:58] ~^ -93: [02:03:58] 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]' -93: [02:03:58] reactant 2 has no mapped atoms. -93: [02:03:58] >> Atoms within one molecule have different RXN roles. -93: [02:03:58] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [02:03:58] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [02:03:58] reactant 0 has no mapped atoms. -93: [02:03:58] reactant 1 has no mapped atoms. -93: [02:03:58] reactant 3 has no mapped atoms. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 5 found multiple times. -93: [02:03:58] product atom-mapping number 6 found multiple times. -93: [02:03:58] product atom-mapping number 7 found multiple times. -93: [02:03:58] product atom-mapping number 8 found multiple times. -93: [02:03:58] product atom-mapping number 12 found multiple times. -93: [02:03:58] product atom-mapping number 9 found multiple times. -93: [02:03:58] product atom-mapping number 10 found multiple times. -93: [02:03:58] product atom-mapping number 11 found multiple times. -93: [02:03:58] reactant 0 has no mapped atoms. -93: [02:03:58] reactant 1 has no mapped atoms. -93: [02:03:58] reactant 3 has no mapped atoms. -93: [02:03:58] reactant atom-mapping number 19 found multiple times. -93: [02:03:58] reactant atom-mapping number 25 found multiple times. -93: [02:03:58] reactant atom-mapping number 20 found multiple times. -93: [02:03:58] reactant atom-mapping number 21 found multiple times. -93: [02:03:58] reactant atom-mapping number 22 found multiple times. -93: [02:03:58] reactant atom-mapping number 23 found multiple times. -93: [02:03:58] reactant atom-mapping number 24 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [22:06:10] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [22:06:10] SMILES Parse Error: check for mistakes around position 2: +93: [22:06:10] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [22:06:10] ~^ +93: [22:06:10] 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]' +93: [22:06:10] reactant 2 has no mapped atoms. +93: [22:06:10] >> Atoms within one molecule have different RXN roles. +93: [22:06:10] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [22:06:10] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [22:06:10] reactant 0 has no mapped atoms. +93: [22:06:10] reactant 1 has no mapped atoms. +93: [22:06:10] reactant 3 has no mapped atoms. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 5 found multiple times. +93: [22:06:10] product atom-mapping number 6 found multiple times. +93: [22:06:10] product atom-mapping number 7 found multiple times. +93: [22:06:10] product atom-mapping number 8 found multiple times. +93: [22:06:10] product atom-mapping number 12 found multiple times. +93: [22:06:10] product atom-mapping number 9 found multiple times. +93: [22:06:10] product atom-mapping number 10 found multiple times. +93: [22:06:10] product atom-mapping number 11 found multiple times. +93: [22:06:10] reactant 0 has no mapped atoms. +93: [22:06:10] reactant 1 has no mapped atoms. +93: [22:06:10] reactant 3 has no mapped atoms. +93: [22:06:10] reactant atom-mapping number 19 found multiple times. +93: [22:06:10] reactant atom-mapping number 25 found multiple times. +93: [22:06:10] reactant atom-mapping number 20 found multiple times. +93: [22:06:10] reactant atom-mapping number 21 found multiple times. +93: [22:06:10] reactant atom-mapping number 22 found multiple times. +93: [22:06:10] reactant atom-mapping number 23 found multiple times. +93: [22:06:10] reactant atom-mapping number 24 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 5 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 5 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 5 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 5 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 5 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 5 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 5 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 5 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 4 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 4 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:03:58] product atom-mapping number 3 found multiple times. -93: [02:03:58] product atom-mapping number 2 found multiple times. -93: [02:03:58] product atom-mapping number 1 found multiple times. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. +93: [22:06:10] product atom-mapping number 3 found multiple times. +93: [22:06:10] product atom-mapping number 2 found multiple times. +93: [22:06:10] product atom-mapping number 1 found multiple times. +93: [22:06:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [02:03:58] product atom-mapping number 6 not found in reactants. -93: [02:03:58] product atom-mapping number 7 not found in reactants. -93: [02:03:58] product atom-mapping number 8 not found in reactants. -94: [02:03:58] ------------------------------------- -94: [02:03:58] Test Reaction StructuralFingerprint -94: [02:03:58] ------------------------------------- -94: [02:03:58] Test Reaction DifferenceFingerprint - 67/236 Test #62: smiTestCatch ........................... Passed 0.26 sec - 68/236 Test #66: depictorCatch .......................... Passed 0.25 sec - 69/236 Test #73: testGeneralFileReader .................. Passed 0.20 sec -test 109 - Start 109: testFragCatalog - -109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog -109: Test timeout computed to be: 1500 -test 110 - Start 110: pyFragCatalog - -110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -110: Test timeout computed to be: 1500 -test 111 - Start 111: testDescriptors - -111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 -93: [02:03:58] product atom-mapping number 7 not found in reactants. -93: [02:03:58] product atom-mapping number 8 not found in reactants. -93: [02:03:58] product atom-mapping number 9 not found in reactants. -93: [02:03:58] product atom-mapping number 10 not found in reactants. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. +93: [22:06:10] product atom-mapping number 6 not found in reactants. +93: [22:06:10] product atom-mapping number 7 not found in reactants. +93: [22:06:10] product atom-mapping number 8 not found in reactants. +93: [22:06:10] product atom-mapping number 7 not found in reactants. +93: [22:06:10] product atom-mapping number 8 not found in reactants. +93: [22:06:10] product atom-mapping number 9 not found in reactants. +93: [22:06:10] product atom-mapping number 10 not found in reactants. +93: [22:06:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [02:03:58] product atom-mapping number 7 not found in reactants. -93: [02:03:58] product atom-mapping number 8 not found in reactants. -93: [02:03:58] product atom-mapping number 9 not found in reactants. -93: [02:03:58] product atom-mapping number 10 not found in reactants. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. +93: [22:06:10] product atom-mapping number 7 not found in reactants. +93: [22:06:10] product atom-mapping number 8 not found in reactants. +93: [22:06:10] product atom-mapping number 9 not found in reactants. +93: [22:06:10] product atom-mapping number 10 not found in reactants. +93: [22:06:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: 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] 93: 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] - 70/236 Test #94: testReactionFingerprints ............... Passed 0.12 sec -60: Test -60: -60: Mrtx1719_3d.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop1.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop2.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop3.cxsmi -60: -60: Test -60: -60: Mrtx1719_atrop4.cxsmi -60: -60: Test -60: -60: Mrtx1719_atropBad1.cxsmi -60: -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [22:06:11] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -20822,124 +20955,99 @@ 100: replaceSub smi1:CCNCC 100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -100: [02:03:58] SMARTS Parse Error: syntax error while parsing: bar -100: [02:03:58] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -96: Randomness seeded to: 3219972094 -96: [02:03:58] atom 0 in product 0 has multiple charge specifications. -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [02:03:58] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [02:03:58] mapped atoms in the reactants were not mapped in the products. +100: [22:06:10] SMARTS Parse Error: syntax error while parsing: bar +100: [22:06:10] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 70/236 Test #83: cdxmlParserCatchTest ................... Passed 0.41 sec + 71/236 Test #94: testReactionFingerprints ............... Passed 0.28 sec +test 110 + Start 110: pyFragCatalog + +110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +110: Test timeout computed to be: 1500 +test 111 + Start 111: testDescriptors + +111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 + 72/236 Test #100: testChemTransforms ..................... Passed 0.18 sec +72: [22:06:10] Finished: testGitHub2285() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [22:06:10] ERROR: Smiles parse error on line 1 +72: [22:06:10] ERROR: Cannot create molecule from : 'c1ccccc' +72: [22:06:10] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [22:06:10] SMILES Parse Error: check for mistakes around position 2: +72: [22:06:10] C(C +72: [22:06:10] ~^ +72: [22:06:10] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [22:06:10] ERROR: Smiles parse error on line 3 +72: [22:06:10] ERROR: Cannot create molecule from : 'C(C' +72: [22:06:10] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule on line 5 +72: [22:06:10] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [22:06:10] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule ending on line 21 +72: [22:06:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule ending on line 21 +72: [22:06:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule ending on line 21 +72: [22:06:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Atom line too short: ' -9.6' on line 28 +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Could not sanitize molecule ending on line 21 +72: [22:06:10] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [22:06:10] ERROR: Atom line too short: ' -9.6' on line 28 +72: [22:06:10] ERROR: moving to the beginning of the next molecule +72: [22:06:10] Finished: testGitHub2479() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [22:06:10] Finished: testGitHub2881() +72: [22:06:10] ----------------------------------------- +72: +72: [22:06:10] ----------------------------------------- +72: [22:06:10] Finished: testGitHub3517() +72: [22:06:10] ----------------------------------------- +72: + 73/236 Test #72: testMolSupplier ........................ Passed 0.57 sec +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [22:06:10] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +96: Randomness seeded to: 2001112121 +96: [22:06:10] atom 0 in product 0 has multiple charge specifications. +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [22:06:10] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [22:06:11] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [02:03:58] mapped atoms in the reactants were not mapped in the products. +96: [22:06:11] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [02:03:58] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [02:03:58] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [02:03:58] mapped atoms in the reactants were not mapped in the products. +96: [22:06:11] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [22:06:11] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [22:06:11] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [02:03:58] product atom-mapping number 2 not found in reactants. -96: [02:03:58] mapped atoms in the reactants were not mapped in the products. +96: [22:06:11] product atom-mapping number 2 not found in reactants. +96: [22:06:11] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [02:03:58] product atom-mapping number 2 not found in reactants. -96: [02:03:58] CX Extensions: Substance group hierarchy is not always preserved. -96: [02:03:58] CX Extensions: Substance group hierarchy is not always preserved. -96: [02:03:58] reactant 0 has no mapped atoms. -96: [02:03:58] product 0 has no mapped atoms. -96: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [02:03:58] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: -101: Randomness seeded to: 2527822924 -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x000056382EB34596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x000056382EB34596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x000056382EB34596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: +96: [22:06:11] product atom-mapping number 2 not found in reactants. +96: [22:06:11] CX Extensions: Substance group hierarchy is not always preserved. +96: [22:06:11] CX Extensions: Substance group hierarchy is not always preserved. +95: 30000000 30000000 104: ----------------------- 104: Subgraph retrieval 104: Finished @@ -20963,13 +21071,6 @@ 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished - 71/236 Test #105: testSubgraphs2 ......................... Passed 0.06 sec -106: Randomness seeded to: 363656623 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: - 72/236 Test #106: subgraphsCatch ......................... Passed 0.05 sec test 112 Start 112: testAUTOCORR2D @@ -20982,192 +21083,23 @@ 113: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -72: [02:03:58] Finished: testSDWriter() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSDSupplierEnding() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSuppliersEmptyFile() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testCisTrans() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testStereoRound() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:03:58] Finished: testIssue226() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testTDTSupplier1() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testTDTSupplier2() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testTDTSupplier3() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSDSupplierFromText() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Spurious data before the first property will be ignored -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Finished: testSDSupplierStrLax1() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Finished: testSDSupplierStrLax2() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Spurious data before the first property will be ignored -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Finished: testSDSupplierFromTextStrLax1() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: Problems encountered parsing data fields -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Property will be truncated after the first blank line -72: [02:03:58] Finished: testSDSupplierFromTextStrLax2() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testIssue265() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: End of data field name not found -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule ending on line 16 -72: [02:03:58] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [02:03:58] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] ERROR: Bond line too short: 'M END' on line 18 -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Finished: testSDErrorHandling() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testIssue381() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -80: [02:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [02:03:58] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[02:03:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [02:03:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 73/236 Test #96: rxnTestCatch ........................... Passed 0.13 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -83: [02:03:58] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [02:03:58] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [02:03:58] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [02:03:58] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [02:03:58] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: -30: ......[02:03:58] Molecule does not have explicit Hs. Consider calling AddHs() -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x000056382EB34596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -101: [02:03:58] Incomplete atom labelling, cannot make bond -101: [02:03:58] +80: [22:06:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [22:06:11] 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.[22:06:11] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [22:06:11] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106: Randomness seeded to: 2375975108 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: +35: [22:06:11] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +101: Randomness seeded to: 2806588401 +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] 101: 101: **** -35: [02:03:58] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -72: [02:03:58] Finished: testSetStreamIndices() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testMixIterAndRandom() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: build: -114: [02:03:58] ------------------------------------- -114: [02:03:58] Basic BCUT tests. - 74/236 Test #100: testChemTransforms ..................... Passed 0.13 sec -72: [02:03:58] Finished: testRemoveHs() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -112: [02:03:58] ---------------------------- -112: start test autocorr2D -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Crippen parameter acquisition. 101: Invariant Violation 101: molzip: bond info already exists for end atom with label:1 101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp @@ -21178,178 +21110,128 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x000056382EB34596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x000055695CF23596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: +30: ......[22:06:11] Molecule does not have explicit Hs. Consider calling AddHs() + 74/236 Test #105: testSubgraphs2 ......................... Passed 0.13 sec + 75/236 Test #106: subgraphsCatch ......................... Passed 0.11 sec +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +96: [22:06:11] reactant 0 has no mapped atoms. +96: [22:06:11] product 0 has no mapped atoms. +96: [22:06:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [22:06:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [22:06:11] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 76/236 Test #96: rxnTestCatch ........................... Passed 0.31 sec +60: Test +60: +60: Sotorasib_3d.cxsmi +60: +60: Test +60: +60: ZM374979_atrop1.cxsmi +60: +60: Test +60: +60: ZM374979_atrop2.cxsmi +60: +60: Test +60: +60: ZM374979_atrop3.cxsmi +60: +60: Test +60: +60: ZM374979_atrop4.cxsmi +60: +60: Test +60: +60: ZM374979_atropBad1.cxsmi +60: +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 - 75/236 Test #83: cdxmlParserCatchTest ................... Passed 0.22 sec -72: [02:03:58] Finished: testGetItemText() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Crippen calculation. -101: [02:03:58] +109: 21 +65: [22:06:11] Warning: stereochemistry around double bond may be incorrect in depiction. +93: [22:06:11] product atom-mapping number 17 not found in reactants. +93: [22:06:11] product atom-mapping number 18 not found in reactants. +93: [22:06:11] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] 101: 101: **** 101: Invariant Violation -101: molzip: zipped Bond already exists, perhaps labels are duplicated -101: Violation occurred on line 744 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b 101: ---------- 101: Stacktrace: 101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x000056382EB2987D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x000056382EB86168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x000056382EB86C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x000056382EB87100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x000056382EB58903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x000056382EB58C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x000056382EB2875E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x00007FDF5B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 14# 0x000056382EB287A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 4# 0x000055695CF23596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: =============================================================================== -101: All tests passed (675 assertions in 10 test cases) -101: -test 117 - Start 117: testRDFcustom - -117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [02:03:58] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -95: 30000000 30000000 -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Issue262: problems with Crippen calculation from pickles. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test AMW calculation. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Exact MW calculation. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Labute ASA descriptors. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test TPSA descriptors. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -114: [02:03:58] done -114: [02:03:58] ------------------------------------- -114: [02:03:58] Larger BCUT tests. - 76/236 Test #101: chemTransformsTestCatch ................ Passed 0.15 sec - 77/236 Test #113: testATF ................................ Passed 0.05 sec -test 118 - Start 118: testRDF - -118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -test 119 - Start 119: testMORSE - -119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -116: [02:03:58] ------------------------------------- -116: [02:03:58] Basic PBF tests. -72: [02:03:58] Finished: testForwardSDSupplier() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testMissingCRSDSupplier() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testIssue3482695() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Finished: testIssue3525673() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testBlankLinesInProps() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testSkipLines() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testGitHub23() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testGitHub88() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -93: [02:03:58] product atom-mapping number 17 not found in reactants. -93: [02:03:58] product atom-mapping number 18 not found in reactants. -93: [02:03:58] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -115: =>start test EEM -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: 21 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: Finished -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Crippen parameter acquisition. +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Crippen calculation. +112: [22:06:11] ---------------------------- +112: start test autocorr2D 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) +101: [22:06:11] Incomplete atom labelling, cannot make bond 107: v = { 107: 0,23}, 107: 1,22}, @@ -21406,73 +21288,13 @@ 107: 11,17}, 107: 12,16}, 107: } -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: Warning: molecule failed filter -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Lipinski parameters. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:03:58] Finished: testGitHub2285() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [02:03:58] ERROR: Smiles parse error on line 1 -72: [02:03:58] ERROR: Cannot create molecule from : 'c1ccccc' -72: [02:03:58] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [02:03:58] SMILES Parse Error: check for mistakes around position 2: -72: [02:03:58] C(C -72: [02:03:58] ~^ -72: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [02:03:58] ERROR: Smiles parse error on line 3 -72: [02:03:58] ERROR: Cannot create molecule from : 'C(C' -72: [02:03:58] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule on line 5 -72: [02:03:58] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:03:58] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule ending on line 21 -72: [02:03:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule ending on line 21 -72: [02:03:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule ending on line 21 -72: [02:03:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Atom line too short: ' -9.6' on line 28 -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Could not sanitize molecule ending on line 21 -72: [02:03:58] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [02:03:58] ERROR: Atom line too short: ' -9.6' on line 28 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [02:03:58] ERROR: moving to the beginning of the next molecule -72: [02:03:58] Finished: testGitHub2479() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [02:03:58] Finished: testGitHub2881() -72: [02:03:58] ----------------------------------------- -72: -72: [02:03:58] ----------------------------------------- -72: [02:03:58] Finished: testGitHub3517() -72: [02:03:58] ----------------------------------------- -72: 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: 1,1}, 107: 2,2}, 107: 3,4}, -90: done 107: 4,5}, 107: 5,6}, 107: 6,7}, @@ -21480,30 +21302,9 @@ 107: 8,9}, 107: 9,14}, 107: 10,15}, -65: [02:03:58] Warning: stereochemistry around double bond may be incorrect in depiction. -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 107: 11,16}, -90: launch2 :1 107: } -90: launch2 :2 107: match = { -90: launch2 :3 - 78/236 Test #72: testMolSupplier ........................ Passed 0.33 sec -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 120 - Start 120: test3D - -120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D -120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -120: Test timeout computed to be: 1500 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: 0,0}, 107: 1,1}, 107: 2,2}, @@ -21517,13 +21318,82 @@ 107: 10,15}, 107: 11,16}, 107: } -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101: [22:06:11] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x000055695CF23596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +114: [22:06:11] ------------------------------------- +114: [22:06:11] Basic BCUT tests. +116: [22:06:11] ------------------------------------- +116: [22:06:11] Basic PBF tests. + 77/236 Test #113: testATF ................................ Passed 0.09 sec +test 117 + Start 117: testRDFcustom + +117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +115: =>start test EEM +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Issue262: problems with Crippen calculation from pickles. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test AMW calculation. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Exact MW calculation. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Labute ASA descriptors. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test TPSA descriptors. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -21532,82 +21402,202 @@ 90: launch3 :1 90: launch3 :2 90: launch3 :3 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: Randomness seeded to: 1736814042 -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -120: [02:03:58] ------------------------------------- -120: [02:03:58] Basic PMI tests. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -75: [02:03:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: Mrtx1719_3d.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop1.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop2.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop3.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop4.cxsmi +60: +60: Test +60: +60: Mrtx1719_atropBad1.cxsmi +60: +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x000055695CF23596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [22:06:11] done +114: [22:06:11] ------------------------------------- +114: [22:06:11] Larger BCUT tests. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: Finished +104: ----------------------- +104: Path retrieval +104: Finished +104: ----------------------- +104: Path retrieval2 +104: Finished +104: ----------------------- +104: Unique Subgraph retrieval +104: Finished +104: ----------------------- +104: testUniqueSubgraphs2 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101: [22:06:11] Incomplete atom labelling, cannot make bond +101: [22:06:11] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 1094 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x000055695CF23596 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +93: [22:06:11] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [22:06:11] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +101: [22:06:11] +101: +101: **** +101: Invariant Violation +101: molzip: zipped Bond already exists, perhaps labels are duplicated +101: Violation occurred on line 744 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 5# 0x000055695CF1887D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x000055695CF75168 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x000055695CF75C88 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x000055695CF76100 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x000055695CF47903 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x000055695CF47C6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x000055695CF1775E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x00007F334B633CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 14# 0x000055695CF177A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [22:06:11] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +101: =============================================================================== +101: All tests passed (675 assertions in 10 test cases) +101: +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +75: [22:06:11] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 75: 0.40201265 0.40201265 75: -0.13299436 -0.13299436 75: 1.00000017 1.00000017 @@ -21629,350 +21619,55 @@ 75: 3.0077234 3.0077234 75: 0.37399312 0.37399312 75: -0.07713336 -0.07713336 -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [02:03:58] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [02:03:58] bond with order 0 found on line 16. This is not part of the MDL specification. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: [02:03:58] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [02:03:58] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: [02:03:58] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: ------------- -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: CCOc1ccccc1 -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 79/236 Test #70: testAtropisomers ....................... Passed 0.44 sec -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -test 121 - Start 121: testWHIM - -121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM -121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -121: Test timeout computed to be: 1500 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [02:03:58] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -91: Randomness seeded to: 2008010784 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: - 80/236 Test #65: testDepictor ........................... Passed 0.49 sec - 81/236 Test #91: substructTestCatch ..................... Passed 0.39 sec -test 122 - Start 122: testGETAWAY - -122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -122: Test timeout computed to be: 1500 -test 123 - Start 123: testAUTOCORR3D - -123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -123: Test timeout computed to be: 1500 + 78/236 Test #101: chemTransformsTestCatch ................ Passed 0.37 sec 30: ... 30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.538s +30: Ran 12 tests in 0.699s 30: 30: OK -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: done -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test GitHub issue 15 -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test GitHub issue 409 -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test chiral matching - 82/236 Test #75: testMolWriter .......................... Passed 0.46 sec -test 124 - Start 124: testCoulombMat - -124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -124: Test timeout computed to be: 1500 -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test dative-bond matching -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test cis/trans matching -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test cis/trans matching part 2 -90: [02:03:58] done -90: [02:03:58] ------------------------------------- -90: [02:03:58] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [02:03:58] done -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [02:03:58] ------------------------------------- -90: [02:03:58] Testing matching E/Z against Cis/Trans stereo bonds -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [02:03:58] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000560D8CE0B38A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000560D8CDFBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F3595433CA8 in /lib/x86_64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x0000560D8CDFBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [02:03:58] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000560D8CDF6420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000560D8CDFBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F3595433CA8 in /lib/x86_64-linux-gnu/libc.so.6 -90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x0000560D8CDFBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test substructure matching with a pathological case for symmetric SSSR -90: [02:03:58] ------------------------------------- -90: [02:03:58] Test isAtomTerminalRGroupOrQueryHydrogen -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -102: Randomness seeded to: 2040997050 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: - 83/236 Test #102: tautomerQueryTestCatch ................. Passed 0.39 sec -test 125 - Start 125: descriptorsTestCatch - -125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -125: Test timeout computed to be: 1500 -124: ===================== Testing CoulombMat ======================= - 84/236 Test #90: testSubstructMatch ..................... Passed 0.46 sec -test 126 - Start 126: pyMolDescriptors - -126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" -126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -126: Test timeout computed to be: 1500 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 85/236 Test #30: pyForceFieldConstraints ................ Passed 0.90 sec -test 127 - Start 127: pyMolDescriptors3D +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 118 + Start 118: testRDF -127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" -127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -127: Test timeout computed to be: 1500 -98: [02:03:58] == testCartesianProduct -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +75: [22:06:11] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [22:06:11] bond with order 0 found on line 16. This is not part of the MDL specification. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: badWedgeError.sdf @@ -22285,45 +21980,20 @@ 68: 68: MulticenterSgroup.mrv 68: -68: [02:03:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [02:03:58] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -124: CM test 1 mat Done -115: 100 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 86/236 Test #124: testCoulombMat ......................... Passed 0.08 sec -test 128 - Start 128: testFingerprints - -128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -67: ..............[02:03:58] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [02:03:58] SMILES Parse Error: check for mistakes around position 1: -67: [02:03:58] invalidsmiles -67: [02:03:58] ^ -67: [02:03:58] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[02:03:58] == testEnumerateLibrary -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test VSA descriptors. +68: [22:06:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [22:06:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +91: Randomness seeded to: 3120705713 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: GenericSgroup.mrv @@ -22356,7 +22026,7 @@ 68: 68: MarvinBadMissingMolID.mrv 68: -68: [02:03:58] +68: [22:06:11] 68: 68: **** 68: Test Assert @@ -22367,12 +22037,12 @@ 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# 0x0000563C3FE9899F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x0000563C3FEA369C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000563C3FE90A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x00007FDCC9C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +68: 2# 0x00005601DB92699F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x00005601DB93169C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x00005601DB91EA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x00007FF623833CA8 in /lib/x86_64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 7# 0x0000563C3FE90BE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 7# 0x00005601DB91EBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: @@ -22381,24 +22051,11 @@ 68: MarvinBadMissingAtomID.mrv 68: 68: Expected id, elementType for an atom definition in MRV file -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test molecular formula calculation. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Issue 3415534. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [02:03:58] done -111: [02:03:58] ------------------------------------- -111: [02:03:58] Test multithreading -111: reading molecules +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadX2.mrv @@ -22431,17 +22088,18 @@ 68: MarvinBadMissingBondOrder.mrv 68: 68: bond must have one of: order, queryType, or convention in MRV File -98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 79/236 Test #91: substructTestCatch ..................... Passed 0.64 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 68: Test 68: 68: MarvinBadMissingSruMolID.mrv 68: 68: Expected a molID in MRV file -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadMissingSruID.mrv @@ -22463,7 +22121,6 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSruID.mrv @@ -22477,10 +22134,6 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSruAtomRef.mrv @@ -22501,37 +22154,42 @@ 68: MarvinBadSupAttachBond.mrv 68: 68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSupAttachOrder.mrv 68: 68: Order for an AttachmentPoint definition must be an integer in MRV file -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -99: .[02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSupMissingAttachBond.mrv @@ -22542,29 +22200,644 @@ 68: MarvinBadSupMissingAttachOrder.mrv 68: 68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -116: [02:03:58] done -116: [02:03:58] ------------------------------------- -116: [02:03:58] PBF edge cases. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [02:03:58] done -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Lipinski parameters. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 80/236 Test #75: testMolWriter .......................... Passed 0.86 sec +test 120 + Start 120: test3D + +120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D +120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +120: Test timeout computed to be: 1500 +70: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 81/236 Test #30: pyForceFieldConstraints ................ Passed 1.11 sec +test 121 + Start 121: testWHIM + +121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM +121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +121: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: Randomness seeded to: 3041707578 +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: done +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test GitHub issue 15 +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test GitHub issue 409 +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test chiral matching +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test dative-bond matching +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test cis/trans matching + 82/236 Test #65: testDepictor ........................... Passed 1.01 sec +test 122 + Start 122: testGETAWAY + +122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +122: Test timeout computed to be: 1500 +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [22:06:11] ------------------------------------- +120: [22:06:11] Basic PMI tests. +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test cis/trans matching part 2 +90: [22:06:11] done +90: [22:06:11] ------------------------------------- +90: [22:06:11] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [22:06:11] done +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 83/236 Test #70: testAtropisomers ....................... Passed 1.00 sec +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [22:06:11] ------------------------------------- +90: [22:06:11] Testing matching E/Z against Cis/Trans stereo bonds +test 123 + Start 123: testAUTOCORR3D + +123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +123: Test timeout computed to be: 1500 +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [22:06:11] +90: +90: **** +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x000055C56030B38A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x000055C5602FBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F55D5433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +90: 8# 0x000055C5602FBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [22:06:11] +90: +90: **** +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x000055C5602F6420 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x000055C5602FBBF1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F55D5433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +90: 8# 0x000055C5602FBD31 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test substructure matching with a pathological case for symmetric SSSR +90: [22:06:11] ------------------------------------- +90: [22:06:11] Test isAtomTerminalRGroupOrQueryHydrogen +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102: Randomness seeded to: 2926857848 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 84/236 Test #90: testSubstructMatch ..................... Passed 0.80 sec + 85/236 Test #102: tautomerQueryTestCatch ................. Passed 0.60 sec +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 124 + Start 124: testCoulombMat + +124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +124: Test timeout computed to be: 1500 +test 125 + Start 125: descriptorsTestCatch + +125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +125: Test timeout computed to be: 1500 +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [22:06:11] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: ..............[22:06:11] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [22:06:11] SMILES Parse Error: check for mistakes around position 1: +67: [22:06:11] invalidsmiles +67: [22:06:11] ^ +67: [22:06:11] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: Cubane.mrv +68: +68: Test +68: +68: FalseAtropisomer.mrv +68: +68: Test +68: +68: AtropEnhancedStereo.mrv +68: +68: Test +68: +68: AtropManyChirals.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced2.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced3.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced4.mrv +68: +68: Test +68: +68: BMS-986142_3d_chiral.mrv +68: +68: Test +68: +68: BMS-986142_3d.mrv +68: +68: Test +68: +68: BMS-986142_atrop1.mrv +68: +68: Test +68: +68: BMS-986142_atrop2.mrv +68: +68: Test +68: +68: BMS-986142_atrop3.mrv +68: +68: Test +68: +68: BMS-986142_atrop4.mrv +68: +68: Test +68: +68: BMS-986142_atrop5.mrv +68: +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: Test +68: +68: BMS-986142_atrop6.mrv +68: +68: Test +68: +68: BMS-986142_atrop7.mrv +68: +68: Test +68: +68: BMS-986142_atrop8.mrv +68: +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +116: [22:06:11] done +116: [22:06:11] ------------------------------------- +116: [22:06:11] PBF edge cases. +116: [22:06:11] done +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [22:06:11] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +124: ===================== Testing CoulombMat ======================= +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 86/236 Test #116: testPBF ................................ Passed 0.44 sec +test 126 + Start 126: pyMolDescriptors + +126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" +126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +126: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +124: CM test 1 mat Done +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 87/236 Test #124: testCoulombMat ......................... Passed 0.08 sec +test 127 + Start 127: pyMolDescriptors3D + +127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" +127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +127: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [22:06:11] done +112: [22:06:11] ------------------------------------- +112: [22:06:11] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [22:06:11] done + 88/236 Test #112: testAUTOCORR2D ......................... Passed 0.54 sec +test 128 + Start 128: testFingerprints + +128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +92: Randomness seeded to: 3354210203 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 89/236 Test #92: testGenericGroups ...................... Passed 0.90 sec +test 129 + Start 129: testMHFPFingerprint + +129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +129: Test timeout computed to be: 1500 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: JDQ443_3d.mrv +68: +68: Test +68: +68: JDQ443_atrop1.mrv +68: +68: Test +68: +68: JDQ443_atrop2.mrv +68: +68: Test +68: +68: JDQ443_atrop3.mrv +68: +68: Test +68: +68: JDQ443_atropBad1.mrv +68: +68: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +125: Randomness seeded to: 85415448 +125: Warning: Atom Count for residue GLU5A does not match expected count +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: RP-6306_atrop1.mrv +68: +68: Test +68: +68: RP-6306_atrop2.mrv +68: +68: Test +68: +68: RP-6306_atrop3.mrv +68: +68: Test +68: +68: RP-6306_atrop4.mrv +68: +68: Test +68: +68: RP-6306_atrop5.mrv +68: +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [22:06:11] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +125: Warning: Atom Count for residue ASN39A does not match expected count +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 90/236 Test #107: filterCatalogTest ...................... Passed 0.66 sec +test 130 + Start 130: testFingerprintGenerators + +130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +130: Test timeout computed to be: 1500 128: 128: 128: @@ -22585,481 +22858,14 @@ 128: 128: 128: ------------------- -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. 128: Atoms: -99: [02:03:58] product 0 has no mapped atoms. 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. 128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. 128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. 128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 87/236 Test #116: testPBF ................................ Passed 0.39 sec -test 129 - Start 129: testMHFPFingerprint - -129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -129: Test timeout computed to be: 1500 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: () -99: ******************************************** -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M RGP 1 1 2 -99: V 1 [*:2] -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 1 2 1 0 -99: M RGP 2 1 1 2 2 -99: V 1 [*:1] -99: V 2 [*:2] -99: M END -99: -99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M RGP 1 1 2 -99: V 1 [*:2] -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 1 2 1 0 -99: M RGP 2 1 1 2 2 -99: V 1 [*:1] -99: V 2 [*:2] -99: M END -99: -99: ******************************************** -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 * -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M RGP 1 1 2 -99: V 1 * -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M RGP 2 1 1 2 2 -99: V 1 * -99: V 2 * -99: M END -99: -99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M RGP 1 1 2 -99: V 1 [*:2] -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 1 2 1 0 -99: M RGP 2 1 1 2 2 -99: V 1 [*:1] -99: V 2 [*:2] -99: M END -99: -99: ******************************************** -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 1 2 1 -99: V 1 halogen.bromine.aromatic -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M ISO 1 1 2 -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 2 1 1 2 2 -99: M END -99: -99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M RGP 1 1 2 -99: V 1 [*:2] -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 -99: 1 2 1 0 -99: M RGP 2 1 1 2 2 -99: V 1 [*:1] -99: V 2 [*:2] -99: M END -99: -99: ******************************************** -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 1 2 1 -99: V 1 halogen.bromine.aromatic -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M ISO 1 1 3 -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 -99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 2 1 1 2 2 -99: M END -99: [02:03:58] reactant 0 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] product 0 has no mapped atoms. -99: [02:03:58] Could not find RLabel mapping for atom: 0 in template: 1 -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: [02:03:58] reactant 1 has no mapped atoms. -99: .. -99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.049s -99: -99: OK -99: -99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -99: $RXN -99: -99: RDKit -99: -99: 2 1 -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 1 0 0 0 0 0 0999 V2000 -99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 1 2 1 0 -99: M RGP 1 2 1 -99: V 1 halogen.bromine.aromatic -99: V 2 [*:1] -99: M STY 1 1 DAT -99: M SAL 1 1 1 -99: M SED 1 [#35&$([Br&$(Br-&!@c)])] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 4 3 0 1 0 0 0 0 0 0999 V2000 -99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -99: 2 3 1 0 -99: 1 2 1 0 -99: 2 4 1 0 -99: M ISO 1 1 3 -99: V 2 boronicacid -99: M STY 1 1 DAT -99: M SAL 1 1 2 -99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -99: M END -99: $MOL -99: -99: RDKit 2D -99: -99: 2 1 0 0 0 0 0 0 0 0999 V2000 -99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -99: 1 2 1 0 -99: M ISO 1 2 2 -99: M RGP 1 1 1 -99: V 1 [*:1] -99: M END -99: -99: $RXN Failed 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 @@ -23209,8 +23015,6 @@ 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: Bonds: @@ -23367,17 +23171,6 @@ 128: 2 2->3 order: a conj?: 1 aromatic?: 1 128: 3 3->4 order: 1 conj?: 1 128: 4 3->5 order: a conj?: 1 aromatic?: 1 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.125s -103: -103: OK -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: 5 5->6 order: a conj?: 1 aromatic?: 1 128: 6 6->7 order: 1 conj?: 1 128: 7 1->8 order: a conj?: 1 aromatic?: 1 @@ -23528,40 +23321,136 @@ 128: 128: ------------------- 128: -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Randomness seeded to: 2332714400 -125: Warning: Atom Count for residue GLU5A does not match expected count -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue ASN39A does not match expected count -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -129: [02:03:58] ------------------------------------- -129: [02:03:58] Test MHFP fingerprint encoder initialization - 88/236 Test #107: filterCatalogTest ...................... Passed 0.51 sec -test 130 - Start 130: testFingerprintGenerators - -130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -130: Test timeout computed to be: 1500 -97: ...[02:03:58] +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +129: [22:06:11] ------------------------------------- +129: [22:06:11] Test MHFP fingerprint encoder initialization +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:11] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Morgan Fingerprints. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Morgan Fingerprints using fromAtoms argument. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Morgan Fingerprints as bit vects. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Morgan Fingerprints with feature invariants. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test additional Morgan fingerprints options. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Atom Codes. +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Atom Pairs. +128: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Atom Pairs part 2. +128: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Topological Torsions. +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] done +128: [22:06:11] ------------------------------------- +128: [22:06:11] Test Bulk Topological Torsions. +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [22:06:11] reactant 0 has no mapped atoms. +93: [22:06:11] product 0 has no mapped atoms. +93: [22:06:11] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ...[22:06:11] 97: 97: **** -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue GLU53A does not match expected count -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue ARG64A does not match expected count -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue LYS80A does not match expected count -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: launch :3 +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.079s +110: +110: OK 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23593,7 +23482,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FD9E743C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F56D1B4A62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23604,17 +23493,17 @@ 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FD9E51B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FD9E51B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FD9E51B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FD9E51B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FD9E51B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F56CF7B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F56CF7B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F56CF7B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F56CF7B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F56CF7B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FD9E74393C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F56D1B473C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005C30D9 in /usr/bin/python3 @@ -23646,17 +23535,675 @@ 97: 75# 0x00000000006820AE in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FD9E7E41CA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007F56D254FCA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: -97: [02:03:58] +97: [22:06:11] 97: 97: **** -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: .[22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 91/236 Test #93: testReaction ........................... Passed 1.00 sec +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.105s +103: +103: OK +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test atom-pair fp generator +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test atom-pair fp generator with different arguments +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] DEPRECATION WARNING: please use AtomPairGenerator +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test atom-pair additional output +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Folded Atom Pairs. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Rooted Atom Pairs. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test ignoring atoms in Atom Pairs. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Atom Pairs including info about chirality. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Morgan Fingerprints. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test morgan fp generator +99: .[22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: () +99: ******************************************** +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M RGP 1 1 2 +99: V 1 [*:2] +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 1 2 1 0 +99: M RGP 2 1 1 2 2 +99: V 1 [*:1] +99: V 2 [*:2] +99: M END +99: +99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M RGP 1 1 2 +99: V 1 [*:2] +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 1 2 1 0 +99: M RGP 2 1 1 2 2 +99: V 1 [*:1] +99: V 2 [*:2] +99: M END +99: +99: ******************************************** +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 * +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M RGP 1 1 2 +99: V 1 * +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M RGP 2 1 1 2 2 +99: V 1 * +99: V 2 * +99: M END +99: +99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M RGP 1 1 2 +99: V 1 [*:2] +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 1 2 1 0 +99: M RGP 2 1 1 2 2 +99: V 1 [*:1] +99: V 2 [*:2] +99: M END +99: +99: ******************************************** +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 1 2 1 +99: V 1 halogen.bromine.aromatic +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M ISO 1 1 2 +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 2 1 1 2 2 +99: M END +99: +99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M RGP 1 1 2 +99: V 1 [*:2] +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 +99: 1 2 1 0 +99: M RGP 2 1 1 2 2 +99: V 1 [*:1] +99: V 2 [*:2] +99: M END +99: +99: ******************************************** +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 1 2 1 +99: V 1 halogen.bromine.aromatic +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M ISO 1 1 3 +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 +99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 2 1 1 2 2 +99: M END +99: [22:06:11] reactant 0 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] product 0 has no mapped atoms. +99: [22:06:11] Could not find RLabel mapping for atom: 0 in template: 1 +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: [22:06:11] reactant 1 has no mapped atoms. +99: .. +99: ---------------------------------------------------------------------- +99: Ran 4 tests in 0.049s +99: +99: OK +99: +99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +99: $RXN +99: +99: RDKit +99: +99: 2 1 +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 1 0 0 0 0 0 0999 V2000 +99: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +99: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 1 2 1 0 +99: M RGP 1 2 1 +99: V 1 halogen.bromine.aromatic +99: V 2 [*:1] +99: M STY 1 1 DAT +99: M SAL 1 1 1 +99: M SED 1 [#35&$([Br&$(Br-&!@c)])] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 4 3 0 1 0 0 0 0 0 0999 V2000 +99: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +99: 2 3 1 0 +99: 1 2 1 0 +99: 2 4 1 0 +99: M ISO 1 1 3 +99: V 2 boronicacid +99: M STY 1 1 DAT +99: M SAL 1 1 2 +99: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +99: M END +99: $MOL +99: +99: RDKit 2D +99: +99: 2 1 0 0 0 0 0 0 0 0999 V2000 +99: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +99: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +99: 1 2 1 0 +99: M ISO 1 2 2 +99: M RGP 1 1 1 +99: V 1 [*:1] +99: M END +99: +99: $RXN Failed +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +104: Finished +129: [22:06:11] done +129: [22:06:11] ------------------------------------- +129: [22:06:11] Test MHFP shingling creation +98: [22:06:11] == testCartesianProduct +98: .[22:06:11] == testEnumerateLibrary 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23688,7 +24235,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FD9E743C62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F56D1B4A62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23699,17 +24246,17 @@ 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FD9E51B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FD9E51B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FD9E51B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FD9E51B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FD9E51B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F56CF7B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F56CF7B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F56CF7B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F56CF7B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F56CF7B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FD9E74393C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F56D1B473C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 97: 47# _PyObject_MakeTpCall in /usr/bin/python3 97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 97: 49# 0x00000000005C30D9 in /usr/bin/python3 @@ -23741,214 +24288,763 @@ 97: 75# 0x00000000006820AE in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FD9E7E41CA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007F56D254FCA8 in /lib/x86_64-linux-gnu/libc.so.6 97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 97: 80# _start in /usr/bin/python3 97: ---------- 97: **** 97: -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue GLU150A does not match expected count -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 89/236 Test #99: pyChemReactionSanitize ................. Passed 0.61 sec -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue ASN157A does not match expected count -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Morgan Fingerprints. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Morgan Fingerprints using fromAtoms argument. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Morgan Fingerprints as bit vects. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Morgan Fingerprints with feature invariants. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test additional Morgan fingerprints options. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Atom Codes. -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Atom Pairs. -128: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Atom Pairs part 2. -128: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Topological Torsions. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] done -128: [02:03:58] ------------------------------------- -128: [02:03:58] Test Bulk Topological Torsions. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 1.004s +67: +67: OK test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -98: ..[02:03:58] == testRGroupState -98: .[02:03:58] == testRandomEnumerateAllBBsLibrary -129: [02:03:58] done -129: [02:03:58] ------------------------------------- -129: [02:03:58] Test MHFP shingling creation -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test atom-pair fp generator -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.534s -67: -67: OK -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: .........[02:03:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:03:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:03:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [02:03:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[02:03:58] product atom-mapping number 1 found multiple times. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 90/236 Test #103: pyTautomerQuery ........................ Passed 0.63 sec + 92/236 Test #103: pyTautomerQuery ........................ Passed 0.91 sec + 93/236 Test #104: testSubgraphs1 ......................... Passed 0.90 sec +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Morgan Fingerprints using fromAtoms argument. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Morgan Fingerprints as bit vects. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test Morgan Fingerprints with feature invariants. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test additional Morgan fingerprints options. +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Single atoms setting radius 1 bits in Morgan fingerprints +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test different invariant generator combinations +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test invariant overriding +130: [22:06:11] done +130: [22:06:11] ------------------------------------- +130: [22:06:11] Test RDKit fp generator +129: [22:06:11] done +129: [22:06:11] ------------------------------------- +129: [22:06:11] Test MHFP hashing of string and uint arrays +129: [22:06:11] done +129: [22:06:11] ------------------------------------- +129: [22:06:11] Test SECFP fingerprint functionality +98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [02:03:58] done -112: [02:03:58] ------------------------------------- -112: [02:03:58] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [02:03:58] done -97: [02:03:58] product atom-mapping number 1 found multiple times. - 91/236 Test #112: testAUTOCORR2D ......................... Passed 0.57 sec -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test atom-pair fp generator with different arguments -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[02:03:58] == testRandomEnumerateLibrary -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [02:03:58] done -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [02:03:58] ------------------------------------- -129: [02:03:58] Test MHFP hashing of string and uint arrays -129: [02:03:58] done -129: [02:03:58] ------------------------------------- -129: [02:03:58] Test SECFP fingerprint functionality -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -93: [02:03:58] reactant 0 has no mapped atoms. -93: [02:03:58] product 0 has no mapped atoms. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -93: [02:03:58] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: marvin03.mrv +68: Sotorasib_atropBad1.mrv 68: +68: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 68: Test 68: -68: Cubane.mrv +68: Sotorasib_atropBad2.mrv 68: +68: [22:06:11] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +129: [22:06:11] done +97: .........[22:06:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [22:06:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [22:06:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [22:06:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[22:06:11] product atom-mapping number 1 found multiple times. +97: [22:06:11] product atom-mapping number 1 found multiple times. +97: ................[22:06:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [22:06:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [22:06:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: ..[22:06:11] reactant 2 has no mapped atoms. +97: [22:06:11] reactant 2 has no mapped atoms. +97: [22:06:11] product 1 has no mapped atoms. +97: ........[22:06:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [22:06:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [22:06:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [22:06:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[22:06:11] reactant atom-mapping number 1 found multiple times. +97: [22:06:11] product atom-mapping number 2 not found in reactants. +97: [22:06:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [22:06:11] product atom-mapping number 5 not found in reactants. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test VSA descriptors. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test molecular formula calculation. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Issue 3415534. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [22:06:11] done +111: [22:06:11] ------------------------------------- +111: [22:06:11] Test multithreading +111: reading molecules +131: Randomness seeded to: 2033751921 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +125: Warning: Atom Count for residue GLU5A does not match expected count + 94/236 Test #67: pyDepictor ............................. Passed 1.49 sec + 95/236 Test #99: pyChemReactionSanitize ................. Passed 1.07 sec + 96/236 Test #110: pyFragCatalog .......................... Passed 0.91 sec + 97/236 Test #129: testMHFPFingerprint .................... Passed 0.32 sec + 98/236 Test #131: fpTestCatch ............................ Passed 0.12 sec +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 134 + Start 134: pyTestMHFP + +134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" +134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +134: Test timeout computed to be: 1500 +test 135 + Start 135: testPartialCharges + +135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges +135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges +135: Test timeout computed to be: 1500 +test 136 + Start 136: pyPartialCharges + +136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" +136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap +136: Test timeout computed to be: 1500 +test 137 + Start 137: testMolTransforms + +137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms +137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +137: Test timeout computed to be: 1500 +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:11] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Hashed Atom Pairs. +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Hashed torsions. +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Rooted Atom Pairs. +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test ignoring atoms in Atom Pairs. +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Rooted Topological Torsions. +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test ignoring atoms in Topological Torsions. +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test atom info from morgan fingerprints. +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] ------------------------------------- +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] ------------------------------------- +128: [22:06:12] ------------------------------------- +128: [22:06:12] ------------------------------------- +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Atom Pairs including info about chirality. +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test Topological Torsions including info about chirality. +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test GitHub Issue 151: PatternFingerprint problems +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test 3D atom pairs. +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [22:06:12] done +128: [22:06:12] ------------------------------------- +128: [22:06:12] Test multithreading with the pattern FP +128: reading molecules +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [22:06:11] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [22:06:12] Found a SCD/SED line with missing/empty SDT specification at line 95 +97: ..[22:06:12] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [22:06:12] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [22:06:12] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [22:06:12] reaction has no reactants +97: [22:06:12] reaction has no products +97: [22:06:12] initialization failed +97: [22:06:12] reaction has no reactants +97: [22:06:12] reaction has no products +97: .[22:06:12] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [22:06:12] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [22:06:12] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [22:06:12] reaction has no reactants +97: [22:06:12] reaction has no products +97: [22:06:12] initialization failed +97: [22:06:12] reaction has no reactants +97: [22:06:12] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.389s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +98: ..[22:06:11] == testRGroupState +98: .[22:06:12] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +98: .[22:06:12] == testRandomEnumerateLibrary +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] More PMI/NPR tests. +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] Basic NPR tests. +69: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:12] deprecated group abbreviation ignored on line 24 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [22:06:12] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007F34362C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007F34362D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007F34362D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000564E41090C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000564E410F7372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000564E41077923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007F3435833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x0000564E41077AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +89: [22:06:12] Explicit valence for atom # 9 N, 5, is greater than permitted +121: =>start test WHIM +121: [22:06:12] test on : 365 molecules done +132: Randomness seeded to: 893915048 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: + 99/236 Test #121: testWHIM ............................... Passed 0.71 sec +100/236 Test #132: fpGenTestCatch ......................... Passed 0.27 sec +101/236 Test #135: testPartialCharges ..................... Passed 0.09 sec +98: .[22:06:12] == testRandomSample +test 139 + Start 139: pyMolTransforms + +139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +139: Test timeout computed to be: 1500 +test 140 + Start 140: forceFieldHelpersCatch + +140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch +140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers +140: Test timeout computed to be: 1500 +test 141 + Start 141: testMMFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +141: Test timeout computed to be: 1500 +98: .[22:06:12] == testRandomSampleAllBBs +98: .[22:06:12] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [22:06:12] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[22:06:12] == testRemoveBadMatches +98: .[22:06:12] == testTimings +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +137: *********************************************************** +137: Testing MolTransforms +137: --------------------------------- +137: test1Canonicalization +137: +137: --------------------------------- +137: testGetSetBondLength +137: +137: --------------------------------- +137: testGetSetAngle +137: +137: --------------------------------- +137: testGetSetDihedral +137: +137: --------------------------------- +137: testGetSetDihedralThroughTripleBond +137: +137: --------------------------------- +137: testGithub1262: PMI descriptors incorrect +137: +137: --------------------------------- +137: testGithub1908: CanonicalizeMol() distorting bond lengths +137: +137: --------------------------------- +137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords +137: +137: --------------------------------- +137: testWeightedCentroid +137: +137: *********************************************************** +102/236 Test #137: testMolTransforms ...................... Passed 0.08 sec +test 142 + Start 142: testMMFFForceFieldHelpersMultiThread + +142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread +142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +142: Test timeout computed to be: 1500 +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +138: Randomness seeded to: 1527103741 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +89: [22:06:12] Explicit valence for atom # 3 Al, 6, is greater than permitted 68: Test 68: 68: FalseAtropisomer.mrv @@ -24005,104 +25101,50 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: 200 -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 92/236 Test #93: testReaction ........................... Passed 0.73 sec -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:58] DEPRECATION WARNING: please use AtomPairGenerator -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test atom-pair additional output -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Folded Atom Pairs. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Rooted Atom Pairs. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test ignoring atoms in Atom Pairs. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Atom Pairs including info about chirality. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Morgan Fingerprints. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test morgan fp generator -129: [02:03:58] done -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 134 - Start 134: pyTestMHFP +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +103/236 Test #138: molTransformsTestCatch ................. Passed 0.09 sec +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 143 + Start 143: testUFFForceFieldHelpers -134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" -134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -134: Test timeout computed to be: 1500 - 93/236 Test #129: testMHFPFingerprint .................... Passed 0.19 sec -97: ................[02:03:58] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [02:03:58] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 135 - Start 135: testPartialCharges +143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +143: Test timeout computed to be: 1500 +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104/236 Test #97: pyChemReactions ........................ Passed 1.36 sec +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 144 + Start 144: testCrystalForceField -135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges -135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges -135: Test timeout computed to be: 1500 -98: .[02:03:58] == testRandomSample -98: .[02:03:58] == testRandomSampleAllBBs +144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +144: Test timeout computed to be: 1500 +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [22:06:12] ------------------------------------- +141: [22:06:12] Test MMFF atom types. +69: [22:06:12] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [22:06:12] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +115: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: BMS-986142_atrop6.mrv @@ -24115,236 +25157,46 @@ 68: 68: BMS-986142_atrop8.mrv 68: -68: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +115: Elapsed time: 1.06748 s +115: Errors:0 +115: [22:06:12] test on : 500 molecules done 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: -68: [02:03:58] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: [02:03:58] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Morgan Fingerprints using fromAtoms argument. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Morgan Fingerprints as bit vects. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test Morgan Fingerprints with feature invariants. -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test additional Morgan fingerprints options. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: ..[02:03:58] reactant 2 has no mapped atoms. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [02:03:58] reactant 2 has no mapped atoms. -97: [02:03:58] product 1 has no mapped atoms. -98: .[02:03:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -98: [02:03:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -98: .[02:03:58] == testRemoveBadMatches -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 94/236 Test #67: pyDepictor ............................. Passed 0.90 sec -98: .[02:03:58] == testTimings -test 136 - Start 136: pyPartialCharges - -136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" -136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap -136: Test timeout computed to be: 1500 -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Single atoms setting radius 1 bits in Morgan fingerprints -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test different invariant generator combinations -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test invariant overriding -130: [02:03:58] done -130: [02:03:58] ------------------------------------- -130: [02:03:58] Test RDKit fp generator -131: Randomness seeded to: 209884777 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 95/236 Test #131: fpTestCatch ............................ Passed 0.13 sec -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:58] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: ........[02:03:59] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -test 137 - Start 137: testMolTransforms +68: [22:06:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +140: Randomness seeded to: 828637181 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +105/236 Test #115: testEEM ................................ Passed 1.12 sec +test 145 + Start 145: pyForceFieldHelpers -137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms -137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -137: Test timeout computed to be: 1500 -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [02:03:59] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[02:03:59] reactant atom-mapping number 1 found multiple times. -97: [02:03:59] product atom-mapping number 2 not found in reactants. -97: [02:03:59] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [02:03:59] product atom-mapping number 5 not found in reactants. - 96/236 Test #135: testPartialCharges ..................... Passed 0.06 sec -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 138 - Start 138: molTransformsTestCatch +145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" +145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap +145: Test timeout computed to be: 1500 +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing MMFF builder tools. +143: [22:06:12] ------------------------------------- +143: [22:06:12] Test UFF atom labels. +142: [22:06:12] ------------------------------------- +142: [22:06:12] Test MMFF multithreading +106/236 Test #140: forceFieldHelpersCatch ................. Passed 0.10 sec +test 146 + Start 146: testDistGeomHelpers -138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers +146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +146: Test timeout computed to be: 1500 +123: =>start test autocorr3D +123: [22:06:12] test on : 365 molecules done +89: [22:06:12] Explicit valence for atom # 4 Al, 6, is greater than permitted +144: ------------------------------------- +144: Test CrystalFF torsional term. 68: Test 68: 68: JDQ443_3d.mrv @@ -24365,145 +25217,26 @@ 68: 68: JDQ443_atropBad1.mrv 68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Hashed Atom Pairs. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Hashed torsions. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Rooted Atom Pairs. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test ignoring atoms in Atom Pairs. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Rooted Topological Torsions. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test ignoring atoms in Topological Torsions. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test atom info from morgan fingerprints. -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] ------------------------------------- -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] ------------------------------------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] ------------------------------------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] ------------------------------------- -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Atom Pairs including info about chirality. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test Topological Torsions including info about chirality. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test GitHub Issue 151: PatternFingerprint problems -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Test UFF atom typer. +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing UFF builder tools. +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing UFF builder+minimization. +107/236 Test #123: testAUTOCORR3D ......................... Passed 0.80 sec +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing MMFF builder+minimization. 68: Test 68: 68: RP-6306_atrop1.mrv @@ -24524,128 +25257,22 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [02:03:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:59] Explicit valence for atom # 9 N, 5, is greater than permitted -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test 3D atom pairs. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [02:03:59] done -128: [02:03:59] ------------------------------------- -128: [02:03:59] Test multithreading with the pattern FP -128: reading molecules +68: [22:06:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: 68: RP-6306_atropBad2.mrv 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -138: Randomness seeded to: 4115801758 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: Randomness seeded to: 3306293752 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -125: Warning: Atom Count for residue GLU5A does not match expected count -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 97/236 Test #138: molTransformsTestCatch ................. Passed 0.05 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 139 - Start 139: pyMolTransforms - -139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -139: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 98/236 Test #132: fpGenTestCatch ......................... Passed 0.19 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 140 - Start 140: forceFieldHelpersCatch - -140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch -140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers -140: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [02:03:59] done -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [02:03:59] ------------------------------------- -120: [02:03:59] More PMI/NPR tests. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] Basic NPR tests. -114: [02:03:59] ------------------------------------- -114: [02:03:59] Test empty molecule BCUT. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [02:03:59] Found a SCD/SED line with missing/empty SDT specification at line 95 - 99/236 Test #114: testBCUT ............................... Passed 0.76 sec -test 141 - Start 141: testMMFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -141: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [22:06:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +89: [22:06:12] Explicit valence for atom # 10 Si, 6, is greater than permitted +147: Randomness seeded to: 3224936373 68: Test 68: 68: RP-6306_3d.mrv @@ -24670,170 +25297,50 @@ 68: 68: Sotorasib_atrop5.mrv 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -137: *********************************************************** -137: Testing MolTransforms -137: --------------------------------- -137: test1Canonicalization -137: -137: --------------------------------- -137: testGetSetBondLength -137: -137: --------------------------------- -137: testGetSetAngle -137: -137: --------------------------------- -137: testGetSetDihedral -137: -137: --------------------------------- -137: testGetSetDihedralThroughTripleBond -137: -137: --------------------------------- -137: testGithub1262: PMI descriptors incorrect -137: -137: --------------------------------- -137: testGithub1908: CanonicalizeMol() distorting bond lengths -137: -137: --------------------------------- -137: testGithub4302: native computeCanonicalTransform() generates non-canonical coords -137: -137: --------------------------------- -137: testWeightedCentroid -137: -137: *********************************************************** -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100/236 Test #137: testMolTransforms ...................... Passed 0.13 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 142 - Start 142: testMMFFForceFieldHelpersMultiThread - -142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread -142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -142: Test timeout computed to be: 1500 -97: ..[02:03:59] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [02:03:59] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [22:06:12] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: ---------------------------------- +69: ---------------------------------- 68: Test 68: 68: Sotorasib_atropBad1.mrv 68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -97: [02:03:59] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [02:03:59] reaction has no reactants -97: [02:03:59] reaction has no products -97: [02:03:59] initialization failed -97: [02:03:59] reaction has no reactants -97: [02:03:59] reaction has no products -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [22:06:12] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x0000564E4109DFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000564E410F73EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000564E41077923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007F3435833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x0000564E41077AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [22:06:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 68: Test 68: 68: Sotorasib_atropBad2.mrv 68: -68: [02:03:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -141: [02:03:59] ------------------------------------- -141: [02:03:59] Test MMFF atom types. -121: =>start test WHIM -121: [02:03:59] test on : 365 molecules done -101/236 Test #121: testWHIM ............................... Passed 0.61 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 143 - Start 143: testUFFForceFieldHelpers - -143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -143: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: .[02:03:59] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [02:03:59] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [02:03:59] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing MMFF builder tools. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [02:03:59] reaction has no reactants -97: [02:03:59] reaction has no products -97: [02:03:59] initialization failed -97: [02:03:59] reaction has no reactants -97: [02:03:59] reaction has no products -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.404s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -104: Finished -104: ----------------------- -104: testRootedSubgraphs -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing MMFF builder+minimization. -142: [02:03:59] ------------------------------------- -142: [02:03:59] Test MMFF multithreading -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -140: Randomness seeded to: 3038153568 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:03:59] ------------------------------------- -143: [02:03:59] Test UFF atom labels. -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished -102/236 Test #104: testSubgraphs1 ......................... Passed 0.93 sec -test 144 - Start 144: testCrystalForceField - -144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -144: Test timeout computed to be: 1500 -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Test UFF atom typer. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing UFF builder tools. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing UFF builder+minimization. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103/236 Test #140: forceFieldHelpersCatch ................. Passed 0.12 sec -test 145 - Start 145: pyForceFieldHelpers - -145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" -145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap -145: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -35: [02:03:59] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. +68: [22:06:12] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +146: [22:06:12] ******************************************************** +146: [22:06:12] Testing DistGeomHelpers +146: [22:06:12] --------------------------------- +146: [22:06:12] test2 +146: +146: go +146: ------------------------------------- +146: 68: Test 68: 68: Sotorasib_3d.mrv @@ -24854,40 +25361,7 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:59] Explicit valence for atom # 3 Al, 6, is greater than permitted -144: ------------------------------------- -144: Test CrystalFF torsional term. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -92: Randomness seeded to: 1078314171 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing Issue239. -104/236 Test #92: testGenericGroups ...................... Passed 1.05 sec -test 146 - Start 146: testDistGeomHelpers - -146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers -146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -146: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 68: Test 68: 68: mrtx1719_3d.mrv @@ -24908,18 +25382,46 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing calcEnergy with passed coords. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [22:06:12] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing Issue239. +126: .[22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:12] DEPRECATION WARNING: please use AtomPairGenerator +118: =>start test rdf +118: [22:06:12] test on : 365 molecules done +108/236 Test #118: testRDF ................................ Passed 1.13 sec 142: processing 142: launch :0 142: launch :1 @@ -24934,119 +25436,18 @@ 142: launch :10 142: launch :11 142: launch :12 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :13 142: launch :14 142: launch :15 142: launch :16 142: launch :17 142: launch :18 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :19 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing calcGrad. 142: launch :20 142: launch :21 142: launch :22 142: launch :23 -117: =>start test rdf custom -117: [02:03:59] test on : 365 molecules done -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:59] Explicit valence for atom # 4 Al, 6, is greater than permitted -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing Issue242. -146: [02:03:59] ******************************************************** -146: [02:03:59] Testing DistGeomHelpers -146: [02:03:59] --------------------------------- -146: [02:03:59] test2 -146: -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: go -146: ------------------------------------- -146: -35: F/C=C/Cl -35: [H]/C(F)=C(/[H])Cl -35: F/C=C/Cl -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing UFF special cases. -143: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 0 -35: F/C=C/Cl -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -35: C/C(F)=C(/C)Cl -143: [02:03:59] Testing Issue239. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:03:59] DEPRECATION WARNING: please use AtomPairGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing calcEnergy with passed coords. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105/236 Test #97: pyChemReactions ........................ Passed 1.11 sec -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing github 308: crash during MMFF parameterization . -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing SFIssue1653802. -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Testing SFIssue2378119. -141: [02:03:59] done -141: [02:03:59] ------------------------------------- -141: [02:03:59] Test MMFF force-field parameter getters. -141: [02:03:59] ------------------------------------- -141: [02:03:59] Test MMFF multithreading -126: ..[02:03:59] +126: ..[22:06:12] 126: 126: **** 126: Pre-condition Violation @@ -25058,10 +25459,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x00007F6694C0443A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x00007F6694C14726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x00007F00D8D8143A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x00007F00D8D91726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x00007F6698C0162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x00007F00DCD9562C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -25072,17 +25473,17 @@ 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x00007F66967B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x00007F66967B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x00007F66967B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x00007F66967B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x00007F66967B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x00007F00DA9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x00007F00DA9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x00007F00DA9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x00007F00DA9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x00007F00DA9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x00007F6698BFE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x00007F00DCD923C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 126: 28# _PyObject_MakeTpCall in /usr/bin/python3 126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 30# 0x00000000005C30D9 in /usr/bin/python3 @@ -25114,639 +25515,896 @@ 126: 56# 0x00000000006820AE in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x00007F66994CCCA8 in /lib/x86_64-linux-gnu/libc.so.6 +126: 59# 0x00007F00DD660CA8 in /lib/x86_64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:59] Explicit valence for atom # 10 Si, 6, is greater than permitted -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing calcGrad. -69: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -35: [02:03:59] ----------------------- -35: Testing isRingFused -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/236 Test #144: testCrystalForceField .................. Passed 0.16 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: ...Warning: Atom Count for residue GLU5A does not match expected count -126: Warning: Atom Count for residue ASN39A does not match expected count -126: Warning: Atom Count for residue GLU53A does not match expected count -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing SFIssue1653802. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing SFIssue2378119. -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.040s -134: -134: OK +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [$([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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] 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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [!#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)] +147: [22:06:12] [!#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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: ----------- +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [$([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)] +147: [22:06:12] [$([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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] 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)] +147: [22:06:12] 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)] +147: [22:06:12] [!#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)] +147: [22:06:12] [!#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)] +147: [22:06:12] [!#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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: ----------- +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing UFF special cases. +35: [22:06:12] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Test UFF force-field parameter getters. -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing handling missing parameters. -143: [02:03:59] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [02:03:59] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [02:03:59] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [02:03:59] UFFTYPER: Unrecognized atom type: Cu+1 (0) -69: [02:03:59] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [02:03:59] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007F5E120C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007F5E120D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007F5E120D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x000055ABC3364C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x000055ABC33CB372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x000055ABC334B923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007F5E11633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x000055ABC334BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -107/236 Test #35: graphmolMolOpsTest ..................... Passed 1.59 sec +147: [22:06:12] [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)] +147: [22:06:12] [$([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)] +147: [22:06:12] [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)] +147: [22:06:12] 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)] +147: ----------- +147: ----------- +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +143: [22:06:12] UFFTYPER: Unrecognized charge state for atom: 0 +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing Issue239. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test unfolded version of RDKFP +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test topological torsion fp generator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [$(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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +147: [22:06:12] [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)] +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing calcEnergy with passed coords. 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -141: generating reference data -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -118: =>start test rdf -118: [02:03:59] test on : 365 molecules done -147: Randomness seeded to: 2281319832 +130: [22:06:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test Topological Torsions. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test Folded torsions. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test Bulk Topological Torsions. +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing calcEnergy with passed coords. +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing calcGrad. +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.082s +139: +139: OK +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing SFIssue1653802. +35: F/C=C/Cl +35: [H]/C(F)=C(/[H])Cl +35: F/C=C/Cl +35: F/C=C/Cl +35: C/C(F)=C(/C)Cl +109/236 Test #144: testCrystalForceField .................. Passed 0.38 sec +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing calcGrad. +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing Issue242. +125: Warning: Atom Count for residue ASN39A does not match expected count +89: [22:06:12] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [22:06:12] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [22:06:12] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [22:06:12] Explicit valence for atom # 27 P, 6, is greater than permitted +35: [22:06:12] ----------------------- +35: Testing isRingFused +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] PMI edge cases. +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] NPR edge cases. +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] 3D descriptors. +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] 3D descriptor edge cases. +120: [22:06:12] done +120: [22:06:12] ------------------------------------- +120: [22:06:12] Inertial shape factor. +120: [22:06:12] done +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing SFIssue2378119. +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Test UFF force-field parameter getters. +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing handling missing parameters. +143: [22:06:12] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [22:06:12] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [22:06:12] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [22:06:12] UFFTYPER: Unrecognized atom type: Cu+1 (0) test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -108/236 Test #118: testRDF ................................ Passed 1.00 sec -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.099s -110: -110: OK +110/236 Test #35: graphmolMolOpsTest ..................... Passed 2.52 sec +111/236 Test #120: test3D ................................. Passed 1.45 sec +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing github 308: crash during MMFF parameterization . +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing SFIssue1653802. +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Testing SFIssue2378119. +141: [22:06:12] done +141: [22:06:12] ------------------------------------- +141: [22:06:12] Test MMFF force-field parameter getters. +141: [22:06:12] ------------------------------------- +141: [22:06:12] Test MMFF multithreading +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.123s +134: +134: OK +112/236 Test #134: pyTestMHFP ............................. Passed 0.90 sec +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Testing SFIssue3009337. test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Testing SFIssue3009337. -143: [02:03:59] done -143: [02:03:59] ------------------------------------- -143: [02:03:59] Test UFF multithreading +test 151 + Start 151: molAlignCatchTest + +151: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest +151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +151: Test timeout computed to be: 1500 +113/236 Test #139: pyMolTransforms ........................ Passed 0.77 sec +108: .............[22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +108: [22:06:12] SMILES Parse Error: syntax error while parsing: --- +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] --- +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [22:06:12] dasfsadf +117: =>start test rdf custom +117: [22:06:12] test on : 365 molecules done +126: Warning: Atom Count for residue GLU5A does not match expected count +147: [22:06:12] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +147: [22:06:12] UFFTYPER: Unrecognized charge state for atom: 1 +147: [22:06:12] UFFTYPER: Unrecognized charge state for atom: 1 +147: [22:06:12] UFFTYPER: Unrecognized charge state for atom: 1 +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.551s +127: +127: OK +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test Rooted Topological Torsions. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test ignoring atoms in Topological Torsions. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test Topological Torsions including info about chirality. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [22:06:12] done +130: [22:06:12] ------------------------------------- +130: [22:06:12] Test convenience and bulk fp calculation functions +143: [22:06:12] done +143: [22:06:12] ------------------------------------- +143: [22:06:12] Test UFF multithreading +test 152 + Start 152: pyMolAlign + +152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" +152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap +152: Test timeout computed to be: 1500 +test 153 + Start 153: testFeatures + +153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures +153: Test timeout computed to be: 1500 +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.382s +133: +133: OK 68: Test 68: -68: FalseAtropisomer.mrv +68: AlexRxn.mrv 68: 68: Test 68: -68: AtropEnhancedStereo.mrv +68: BadReactionSign.mrv 68: 68: Test 68: -68: AtropManyChirals.mrv +68: bondArray_node.mrv 68: 68: Test 68: -68: AtropManyChiralsEnhanced.mrv +68: marvin03.mrv 68: 68: Test 68: -68: AtropManyChiralsEnhanced2.mrv +68: marvin04.mrv 68: 68: Test 68: -68: AtropManyChiralsEnhanced3.mrv +68: marvin08.mrv 68: 68: Test 68: -68: AtropManyChiralsEnhanced4.mrv +68: marvin09.mrv 68: 68: Test 68: -68: BMS-986142_3d_chiral.mrv +68: marvin11.mrv 68: 68: Test 68: -68: BMS-986142_3d.mrv +68: marvin05.mrv 68: 68: Test 68: -68: BMS-986142_atrop1.mrv +68: EmptyRxn.mrv 68: +68: [22:06:12] initialization failed +145: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:12] Molecule does not have explicit Hs. Consider calling AddHs() +143: generating reference data +142: done +142: [22:06:12] done +141: generating reference data +108: .[22:06:12] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [22:06:12] SMILES Parse Error: check for mistakes around position 1: +108: [22:06:12] mydoghasfleas +108: [22:06:12] ^ +108: [22:06:12] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +114: [22:06:12] ------------------------------------- +114: [22:06:12] Test empty molecule BCUT. +114/236 Test #114: testBCUT ............................... Passed 1.85 sec +test 154 + Start 154: pyChemicalFeatures + +154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" +154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap +154: Test timeout computed to be: 1500 +153: [22:06:12] ------------------------------------- +153: [22:06:12] AtomType parser testing. +153: [22:06:12] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] FeatureDefinition parser testing. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Test pulling feat defs from a string. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] FeatureDef functionality testing. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] FeatureFactory testing. +153: [22:06:12] 1 +153: [22:06:12] 2 +153: [22:06:12] 3 +153: [22:06:12] 4 +153: [22:06:12] 5 +153: [22:06:12] 6 +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Feature Location testing. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Test building a FeatureFactory from a file +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing Issue 224. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing Issue 225. +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Test Issue346 +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Test Issue347 +153: [22:06:12] done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing Issue 348. +153: [22:06:12] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [22:06:12] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing Nested AtomType definitions. +153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [22:06:12] expect a precondition failure message below +153: [22:06:12] +153: +153: **** +153: Pre-condition Violation +153: molecule has no conformers +153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp +153: Failed Expression: dp_mol->getNumConformers() +153: ---------- +153: Stacktrace: +153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 +153: 4# 0x0000561248B4EE50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000561248B43743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x00007FD25B033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +153: 8# 0x0000561248B43841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: ---------- +153: **** +153: +153: [22:06:12] Done +153: [22:06:12] ------------------------------------- +153: [22:06:12] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [22:06:12] done +109: [22:06:12] +109: +109: **** +109: Invariant Violation +109: nonsense +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FF2670DCDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005559706FD1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005559706FA6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FF266433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005559706FA7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [22:06:12] +109: +109: **** +109: Invariant Violation +109: nonsense no new line +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FF2670DCDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005559706FD1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005559706FA6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FF266433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005559706FA7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [22:06:12] +109: +109: **** +109: Invariant Violation +109: nonsense with tab +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FF2670DCDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005559706FD1FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005559706FA6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FF266433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005559706FA7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: 68: Test 68: -68: BMS-986142_atrop2.mrv +68: RxnNoCoords.mrv 68: 68: Test 68: -68: BMS-986142_atrop3.mrv +68: mrvValenceZero.mrv 68: 68: Test 68: -68: BMS-986142_atrop4.mrv +68: condition_coordinates_mpoint.mrv 68: 68: Test 68: -68: BMS-986142_atrop5.mrv +68: marvin01.mrv 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: 400 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109/236 Test #134: pyTestMHFP ............................. Passed 0.47 sec -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 151 - Start 151: molAlignCatchTest - -151: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest -151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -151: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: generating reference data -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] PMI edge cases. -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] NPR edge cases. -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] 3D descriptors. -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] 3D descriptor edge cases. -120: [02:03:59] done -120: [02:03:59] ------------------------------------- -120: [02:03:59] Inertial shape factor. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: BMS-986142_atrop6.mrv +68: aspirineSynthesisWithAttributes.mrv 68: 68: Test 68: -68: BMS-986142_atrop7.mrv +68: marvin01.mrv 68: 68: Test 68: -68: BMS-986142_atrop8.mrv +68: NewChiralTest 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -120: [02:03:59] done -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110/236 Test #120: test3D ................................. Passed 0.99 sec -test 152 - Start 152: pyMolAlign - -152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" -152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap -152: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111/236 Test #110: pyFragCatalog .......................... Passed 1.13 sec 68: Test 68: -68: BMS-986142_atropBad2.mrv +68: NewChiralTest 68: -68: [02:03:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -test 153 - Start 153: testFeatures - -153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures -153: Test timeout computed to be: 1500 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [02:03:59] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [$([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)] -147: [02:03:59] [$(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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -153: [02:03:59] ------------------------------------- -153: [02:03:59] AtomType parser testing. -153: [02:03:59] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] FeatureDefinition parser testing. -147: [02:03:59] [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)] -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Test pulling feat defs from a string. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] FeatureDef functionality testing. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.187s -136: -136: OK -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] 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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [!#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)] -147: [02:03:59] [!#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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] FeatureFactory testing. -153: [02:03:59] 1 -153: [02:03:59] 2 -153: [02:03:59] 3 -153: [02:03:59] 4 -153: [02:03:59] 5 -153: [02:03:59] 6 -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Feature Location testing. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Test building a FeatureFactory from a file -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing Issue 224. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing Issue 225. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Test Issue346 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Test Issue347 -153: [02:03:59] done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing Issue 348. -153: [02:03:59] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [02:03:59] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing Nested AtomType definitions. -153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [02:03:59] expect a precondition failure message below -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [02:03:59] -153: -153: **** -153: Pre-condition Violation -153: molecule has no conformers -153: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -153: Failed Expression: dp_mol->getNumConformers() -153: ---------- -153: Stacktrace: -153: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x00005585C3C12E50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x00005585C3C07743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x00007F351EC33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -153: 8# 0x00005585C3C07841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: ---------- -153: **** -153: -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -153: [02:03:59] Done -153: [02:03:59] ------------------------------------- -153: [02:03:59] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [02:03:59] done -147: ----------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112/236 Test #153: testFeatures ........................... Passed 0.06 sec -test 154 - Start 154: pyChemicalFeatures - -154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" -154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap -154: Test timeout computed to be: 1500 -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [$([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)] -147: [02:03:59] [$([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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] 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)] -147: [02:03:59] 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)] -147: [02:03:59] [!#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)] -147: [02:03:59] [!#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)] -147: [02:03:59] [!#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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: ----------- -147: [02:03:59] [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)] -147: [02:03:59] [$([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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] 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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: JDQ443_3d.mrv +68: NewChiralTestNoChiral 68: 68: Test 68: -68: JDQ443_atrop1.mrv +68: NewChiralTestNoChiral 68: 68: Test 68: -68: JDQ443_atrop2.mrv +68: NewChiralTest2 68: 68: Test 68: -68: JDQ443_atrop3.mrv +68: NewChiralTest2 68: 68: Test 68: -68: JDQ443_atropBad1.mrv +68: NewChiralTest2AllChiral 68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -147: ----------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [02:03:59] Explicit valence for atom # 2 O, 4, is greater than permitted -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: ----------- -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [$(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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -147: [02:03:59] [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)] -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test unfolded version of RDKFP -126: Warning: Atom Count for residue GLU5A does not match expected count -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test topological torsion fp generator -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -89: [02:03:59] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [02:03:59] Explicit valence for atom # 3 Be, 4, is greater than permitted -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator 68: Test 68: -68: RP-6306_atrop1.mrv +68: NewChiralTest2AllChiral 68: 68: Test 68: -68: RP-6306_atrop2.mrv +68: Vendor839 68: 68: Test 68: -68: RP-6306_atrop3.mrv +68: DoubleBondChain 68: 68: Test 68: -68: RP-6306_atrop4.mrv +68: Na_Mg_Al_OH 68: 68: Test 68: -68: RP-6306_atrop5.mrv +68: Pb 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RP-6306_atropBad1.mrv +68: O_Mg_Si 68: -68: [02:03:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -151: Randomness seeded to: 2676807025 -151: 74954210 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RP-6306_atropBad2.mrv +68: SquiggleBond 68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test Topological Torsions. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test Folded torsions. -115: Elapsed time: 1.21515 s -115: Errors:0 -115: [02:03:59] test on : 500 molecules done -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test Bulk Topological Torsions. -113/236 Test #115: testEEM ................................ Passed 1.25 sec +68: Test +68: +68: BigMacrocycle +68: +68: Test +68: +68: Smiles1 +68: +115/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.80 sec +116/236 Test #153: testFeatures ........................... Passed 0.07 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 156 + Start 156: pyShapeHelpers + +156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +156: Test timeout computed to be: 1500 +125: Warning: Atom Count for residue GLU53A does not match expected count +69: [22:06:13] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [22:06:13] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +117/236 Test #68: testMrvToMol ........................... Passed 2.57 sec +118/236 Test #109: testFragCatalog ........................ Passed 2.19 sec +119/236 Test #127: pyMolDescriptors3D ..................... Passed 1.62 sec +108: ....... +108: ---------------------------------------------------------------------- +108: Ran 21 tests in 1.632s +108: +108: OK +108: (Five aromatic carbons And (Not any of Five aromatic carbons)) +108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) +108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) +108: ******************************************** +108: Testing: PAINS_A 2 +108: ******************************************** +108: Testing: PAINS_B 4 +108: ******************************************** +108: Testing: PAINS_C 8 +108: ******************************************** +108: Testing: PAINS 14 +108: (Not FilterMatcher) +108: Bar +108: Count 1 +108: ******************************************** +108: {'Cl,Br,I'} +108: 1 +108: 2 +108: running +125: Warning: Atom Count for residue ARG64A does not match expected count +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [22:06:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +155: *********************************************************** +155: Testing ShapeHelpers +155: --------------------------------- +155: test1Encode +155: +155: --------------------------------- +155: test2Compare +155: +155: --------------------------------- +155: testGithub4364 +155: +155: *********************************************************** +151: Randomness seeded to: 1656980077 +151: 60704568 +151: 85655682 +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 5 +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 5 +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 5 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -25768,602 +26426,126 @@ 149: testIssue241 149: 149: *********************************************************** -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -142: done -89: [02:03:59] Explicit valence for atom # 27 P, 6, is greater than permitted -114/236 Test #136: pyPartialCharges ....................... Passed 0.64 sec -115/236 Test #149: testMolAlign ........................... Passed 0.23 sec -test 156 - Start 156: pyShapeHelpers - -156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -156: Test timeout computed to be: 1500 test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -145: ..[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -142: [02:03:59] done -151: 55561164 -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [02:03:59] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -125: Warning: Atom Count for residue ASN39A does not match expected count -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [02:03:59] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -116/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.54 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -147: [02:03:59] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -117/236 Test #157: testMolCatalog ......................... Passed 0.06 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -155: *********************************************************** -155: Testing ShapeHelpers -155: --------------------------------- -155: test1Encode -155: -155: --------------------------------- -155: test2Compare -155: -155: --------------------------------- -155: testGithub4364 -155: -155: *********************************************************** -118/236 Test #155: testShapeHelpers ....................... Passed 0.09 sec +120/236 Test #133: pyTestGenerator ........................ Passed 1.34 sec +121/236 Test #149: testMolAlign ........................... Passed 0.60 sec +122/236 Test #155: testShapeHelpers ....................... Passed 0.30 sec +145: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 1 -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 1 -69: [02:03:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [02:03:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 1 -143: processing -143: launch :0 -143: launch :1 -143: launch :2 -143: [02:03:59] Rep: 0 Mol:1 -143: launch :3 -143: [02:03:59] Rep: 0 Mol:3 -68: Test -68: -68: Sotorasib_3d.mrv -68: -68: Test -68: -68: ZM374979_atrop1.mrv -68: -68: Test -68: -68: ZM374979_atrop2.mrv -68: -68: Test -68: -68: ZM374979_atrop3.mrv -68: -68: Test -68: -68: ZM374979_atropBad1.mrv -68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:03:59] Rep: 0 Mol:5 -143: [02:03:59] Rep: 0 Mol:9 -143: [02:03:59] Rep: 0 Mol:2 -143: [02:03:59] Rep: 0 Mol:0 -143: [02:03:59] Rep: 0 Mol:13 -143: [02:03:59] Rep: 0 Mol:4 -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test Rooted Topological Torsions. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test ignoring atoms in Topological Torsions. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -159: ----------------- Test 1 -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test Topological Torsions including info about chirality. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [02:03:59] done -130: [02:03:59] ------------------------------------- -130: [02:03:59] Test convenience and bulk fp calculation functions -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:03:59] Rep: 0 Mol:7 -143: [02:03:59] Rep: 0 Mol:11 -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.073s -139: -139: OK -143: [02:03:59] Rep: 0 Mol:17 -143: [02:03:59] Rep: 0 Mol:15 -143: [02:03:59] Rep: 0 Mol:19 -143: [02:03:59] Rep: 0 Mol:23 -143: [02:03:59] Rep: 0 Mol:27 -143: [02:03:59] Rep: 0 Mol:6 -143: [02:03:59] Rep: 0 Mol:10 -143: [02:03:59] Rep: 0 Mol:31 -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:03:59] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [02:03:59] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: mrtx1719_3d.mrv -68: -68: Test -68: -68: mrtx1719_atrop1.mrv -68: -68: Test -68: -68: mrtx1719_atrop2.mrv -68: -68: Test -68: -68: mrtx1719_atrop3.mrv -68: -68: Test -68: -68: mrtx1719_atropBad1.mrv -68: -68: [02:03:59] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -123: =>start test autocorr3D -123: [02:03:59] test on : 365 molecules done -141: processing -141: launch :0 -141: launch :1 -141: [02:03:59] Rep: 0 Mol:0 -141: launch :2 -141: [02:03:59] Rep: 0 Mol:1 -141: launch :3 -141: [02:03:59] Rep: 0 Mol:2 -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:03:59] Rep: 0 Mol:3 -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:03:59] Rep: 0 Mol:21 -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:03:59] Rep: 0 Mol:5 -143: [02:03:59] Rep: 0 Mol:25 -145: [02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -119/236 Test #123: testAUTOCORR3D ......................... Passed 1.22 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 -145: .[02:03:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 5 -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 5 -143: [02:03:59] Rep: 0 Mol:8 -143: [02:03:59] Rep: 0 Mol:29 -143: [02:03:59] Rep: 0 Mol:12 -141: [02:03:59] Rep: 0 Mol:9 -141: [02:03:59] Rep: 0 Mol:4 -141: [02:03:59] Rep: 0 Mol:6 -141: [02:03:59] Rep: 0 Mol:13 -141: [02:03:59] Rep: 0 Mol:10 -143: [02:03:59] Rep: 0 Mol:14 -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 5 -143: [02:03:59] Rep: 0 Mol:16 -160: Randomness seeded to: 1036947763 -160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -120/236 Test #139: pyMolTransforms ........................ Passed 0.76 sec test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 -141: [02:03:59] Rep: 0 Mol:17 -159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -141: [02:03:59] Rep: 0 Mol:8 -159: Done -159: ----------------- Test 2 -141: [02:03:59] Rep: 0 Mol:12 -143: [02:03:59] Rep: 0 Mol:20 -143: [02:03:59] Rep: 0 Mol:18 -141: [02:03:59] Rep: 0 Mol:16 -125: Warning: Atom Count for residue GLU53A does not match expected count -161: ----------------- Test 1 -145: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:03:59] Rep: 0 Mol:7 -141: [02:03:59] Rep: 0 Mol:11 -143: [02:03:59] Rep: 0 Mol:24 -159: file test2_1.png gave hash 240594419U not the expected 638584804U -148: .[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:03:59] Rep: 0 Mol:14 -141: [02:03:59] Rep: 0 Mol:20 -143: [02:03:59] Rep: 0 Mol:22 -141: [02:03:59] Rep: 0 Mol:15 -141: [02:03:59] Rep: 0 Mol:24 -143: [02:03:59] Rep: 0 Mol:28 -141: [02:03:59] Rep: 0 Mol:19 -141: [02:03:59] Rep: 0 Mol:18 -141: [02:03:59] Rep: 0 Mol:28 -143: [02:03:59] Rep: 0 Mol:26 -159: file test2_2.png gave hash 278647755U not the expected 610424244U -141: [02:03:59] Rep: 0 Mol:23 -141: [02:03:59] Rep: 0 Mol:27 -141: [02:03:59] Rep: 0 Mol:22 -119: =>start test MORSE -119: =>read file -119: [02:03:59] test on : 365 molecules done -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.250s -133: -133: OK -121/236 Test #119: testMORSE .............................. Passed 1.49 sec +69: [22:06:13] Empty atom list: 'M ALS 1 0 F' on line 8. +69: de_DE.UTF-8 +69: [22:06:13] ------------------------------------- +69: [22:06:13] Test multithreading Locale Switching +159: ----------------- Test 1 +123/236 Test #108: pyFilterCatalog ........................ Passed 2.32 sec +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.459s +145: +145: OK test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -141: [02:03:59] Rep: 0 Mol:31 -141: [02:03:59] Rep: 0 Mol:26 -141: [02:03:59] Rep: 0 Mol:21 -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.309s -145: -145: OK -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -69: ---------------------------------- -68: Test -68: -68: AlexRxn.mrv -68: -68: Test -68: -68: BadReactionSign.mrv -68: -68: Test -68: -68: bondArray_node.mrv -68: -68: Test -68: -68: marvin03.mrv -68: -68: Test -68: -68: marvin04.mrv -68: -68: Test -68: -68: marvin08.mrv -68: -68: Test -68: -68: marvin09.mrv -68: -68: Test -68: -68: marvin11.mrv -68: -68: Test -68: -68: marvin05.mrv -68: -68: Test -68: -68: EmptyRxn.mrv -68: -68: [02:03:59] initialization failed -69: ---------------------------------- -141: [02:03:59] Rep: 0 Mol:30 -69: [02:03:59] -69: -69: **** -143: [02:03:59] Rep: 0 Mol:30 -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x000055ABC3371FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x000055ABC33CB3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x000055ABC334B923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007F5E11633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x000055ABC334BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -69: [02:03:59] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:03:59] Rep: 0 Mol:25 -148: ..[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test 4 -148: .[02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue ASN39A does not match expected count -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -141: [02:03:59] Rep: 0 Mol:29 -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 6 -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test4_1.png gave hash 509333604U not the expected 3993974247U -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test 5 -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -122/236 Test #145: pyForceFieldHelpers .................... Passed 0.76 sec +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 6 +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 6 +147: [22:06:13] UFFTYPER: Unrecognized charge state for atom: 6 +124/236 Test #157: testMolCatalog ......................... Passed 0.14 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test5_1.png gave hash 650561118U not the expected 571291290U -147: [02:03:59] UFFTYPER: Unrecognized charge state for atom: 6 -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test5_2.png gave hash 2649140411U not the expected 97265124U -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:03:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -68: Test -68: -68: RxnNoCoords.mrv -68: -68: Test -68: -68: mrvValenceZero.mrv -68: -68: Test -68: -68: condition_coordinates_mpoint.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: aspirineSynthesisWithAttributes.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: NewChiralTest -68: -68: Test -68: -68: NewChiralTest -68: -68: Test -68: -68: NewChiralTestNoChiral -68: -68: Test -68: -68: NewChiralTestNoChiral -68: -68: Test -68: -68: NewChiralTest2 -68: -68: Test -68: -68: NewChiralTest2 -68: -68: Test -68: -68: NewChiralTest2AllChiral -68: -68: Test -68: -68: NewChiralTest2AllChiral -68: -68: Test -68: -68: Vendor839 -68: -68: Test -68: -68: DoubleBondChain -68: -68: Test -68: -68: Na_Mg_Al_OH -68: -68: Test -68: -68: Pb -68: -68: Test -68: -68: O_Mg_Si -68: -68: Test -68: -68: SquiggleBond -68: -68: Test -68: -68: BigMacrocycle -68: -68: Test -68: -68: Smiles1 -68: -154: .[02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -123/236 Test #68: testMrvToMol ........................... Passed 1.90 sec -147: [02:04:00] UFFTYPER: Unrecognized charge state for atom: 6 -159: file test5_3.png gave hash 2951986966U not the expected 606188176U +89: [22:06:13] Explicit valence for atom # 9 N, 5, is greater than permitted +159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U 159: Done -159: ----------------- Test 6 (atom labels) -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U +159: ----------------- Test 2 +126: Warning: Atom Count for residue ASN39A does not match expected count +160: Randomness seeded to: 2919401360 +160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +161: ----------------- Test 1 +159: file test2_1.png gave hash 240594419U not the expected 638584804U +69: [22:06:13] Test multithreading (Done) +69: [22:06:13] ------------------------------------- +60: Test +60: +60: AtropCanon1.cxsmi +60: +60: Test +60: +60: AtropCanon2.cxsmi +60: +60: Test +60: +60: AtropCanon3.cxsmi +60: +60: Test +60: +60: BMS-986142_3d_chiral.cxsmi +60: +60: Test +60: +60: BMS-986142_3d.cxsmi +60: +60: =============================================================================== +60: All tests passed (2496 assertions in 31 test cases) +60: +125/236 Test #60: cxsmilesTest ........................... Passed 2.98 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue ARG64A does not match expected count -160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U -154: .[02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test 7 (backgrounds) -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.385s -127: -127: OK -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.131s -156: -156: OK -156: Testing Shape Helpers wrapper -159: file test7_1.png gave hash 2406197059U not the expected 1322246680U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.436s +136: +136: OK +159: file test2_2.png gave hash 278647755U not the expected 610424244U +125: Warning: Atom Count for residue LYS80A does not match expected count +69: *************************************** +69: *************************************** +69: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [22:06:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -27657,6 +27839,8 @@ 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory +159: Done +159: ----------------- Test 4 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -28329,58 +28513,8 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -126: Warning: Atom Count for residue GLU53A does not match expected count -141: [02:04:00] Rep: 20 Mol:0 -141: [02:04:00] Rep: 20 Mol:4 -141: [02:04:00] Rep: 20 Mol:8 -141: [02:04:00] Rep: 20 Mol:12 -141: [02:04:00] Rep: 20 Mol:16 -141: [02:04:00] Rep: 20 Mol:20 -141: [02:04:00] Rep: 20 Mol:24 -141: [02:04:00] Rep: 20 Mol:28 -141: [02:04:00] Rep: 20 Mol:3 -141: [02:04:00] Rep: 20 Mol:7 -141: [02:04:00] Rep: 20 Mol:11 -141: [02:04:00] Rep: 20 Mol:15 -141: [02:04:00] Rep: 20 Mol:19 -141: [02:04:00] Rep: 20 Mol:23 -141: [02:04:00] Rep: 20 Mol:27 -141: [02:04:00] Rep: 20 Mol:31 -60: Test -60: -60: AtropCanon1.cxsmi -60: -60: Test -60: -60: AtropCanon2.cxsmi -60: -60: Test -60: -60: AtropCanon3.cxsmi -60: -60: Test -60: -60: BMS-986142_3d_chiral.cxsmi -60: -60: Test -60: -60: BMS-986142_3d.cxsmi -60: -60: =============================================================================== -60: All tests passed (2496 assertions in 31 test cases) -60: -159: file test7_2.png gave hash 4033628357U not the expected 1499012715U -159: Done -159: ----------------- Test8: PrepareMolDrawing -159: Done -159: ----------------- Test multi-threaded drawing -159: reading molecules -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U -124/236 Test #60: cxsmilesTest ........................... Passed 2.17 sec -125/236 Test #127: pyMolDescriptors3D ..................... Passed 1.46 sec -126/236 Test #133: pyTestGenerator ........................ Passed 1.20 sec -127/236 Test #165: FMCStest ............................... Passed 0.09 sec +126/236 Test #145: pyForceFieldHelpers .................... Passed 1.24 sec +127/236 Test #165: FMCStest ............................... Passed 0.07 sec test 166 Start 166: molHashCatchTest @@ -28393,95 +28527,85 @@ 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +69: [22:06:13] bond with order 0 found on line 7. This is not part of the MDL specification. +143: processing +143: launch :0 +143: launch :1 +143: launch :2 +143: launch :3 +143: [22:06:13] Rep: 0 Mol:2 +143: [22:06:13] Rep: 0 Mol:0 +143: [22:06:13] Rep: 0 Mol:1 +143: [22:06:13] Rep: 0 Mol:5 +159: file test4_1.png gave hash 509333604U not the expected 3993974247U +159: Done +159: ----------------- Test 5 +119: =>start test MORSE +119: =>read file +119: [22:06:13] test on : 365 molecules done +128/236 Test #119: testMORSE .............................. Passed 2.17 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 +160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U +143: [22:06:13] Rep: 0 Mol:3 +143: [22:06:13] Rep: 0 Mol:4 +143: [22:06:13] Rep: 0 Mol:6 +143: [22:06:13] Rep: 0 Mol:9 +143: [22:06:13] Rep: 0 Mol:10 +159: file test5_1.png gave hash 650561118U not the expected 571291290U +89: [22:06:13] Explicit valence for atom # 3 Al, 6, is greater than permitted +161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U +69: [22:06:13] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [22:06:13] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [22:06:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +129/236 Test #136: pyPartialCharges ....................... Passed 1.47 sec test 169 Start 169: pyMMPA 169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" 169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.014s -158: -158: OK -161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U -128/236 Test #156: pyShapeHelpers ......................... Passed 0.54 sec -test 170 - Start 170: testRascalMCES - -170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 -159: generating reference drawings -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue ARG64A does not match expected count -161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U -154: ..[02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() +143: [22:06:13] Rep: 0 Mol:13 +143: [22:06:13] Rep: 0 Mol:7 +143: [22:06:13] Rep: 0 Mol:11 +69: generating smiles +143: [22:06:13] Rep: 0 Mol:17 +143: [22:06:13] Rep: 0 Mol:15 +143: [22:06:13] Rep: 0 Mol:19 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.013691 seconds +168: Time elapsed 0.005493 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. +143: [22:06:13] Rep: 0 Mol:14 +143: [22:06:13] Rep: 0 Mol:23 +143: [22:06:13] Rep: 0 Mol:27 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 20 Mol:2 -141: [02:04:00] Rep: 20 Mol:6 -129/236 Test #158: pyMolCatalog ........................... Passed 0.55 sec -154: .[02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[02:04:00] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [02:04:00] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.240s -154: -154: OK 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 20 Mol:10 -141: [02:04:00] Rep: 20 Mol:14 -166: Randomness seeded to: 62446918 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -test 171 - Start 171: testRascalCluster - -171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -171: Test timeout computed to be: 1500 +69: 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 +69: converting back 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 20 Mol:18 -141: [02:04:00] Rep: 20 Mol:22 -141: [02:04:00] Rep: 20 Mol:26 -141: [02:04:00] Rep: 20 Mol:30 -130/236 Test #166: molHashCatchTest ....................... Passed 0.11 sec -test 172 - Start 172: pyRascalMCES - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -172: Test timeout computed to be: 1500 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. +143: [22:06:13] Rep: 0 Mol:31 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] @@ -28492,332 +28616,62 @@ 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. +143: [22:06:13] Rep: 0 Mol:8 +143: [22:06:13] Rep: 0 Mol:18 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. -160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U -160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -125: Warning: Atom Count for residue LYS80A does not match expected count -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -108: .............[02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -89: [02:04:00] Explicit valence for atom # 9 N, 5, is greater than permitted -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U -161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf -108: [02:04:00] SMILES Parse Error: syntax error while parsing: --- -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] --- -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [02:04:00] dasfsadf +69: check isomorphism +89: [22:06:13] Explicit valence for atom # 4 Al, 6, is greater than permitted +143: [22:06:13] Rep: 0 Mol:12 +143: [22:06:13] Rep: 0 Mol:22 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.011730 seconds +168: Time elapsed 0.004957 seconds 168: 168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 +126: Warning: Atom Count for residue GLU53A does not match expected count 168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 -109: [02:04:00] -109: -109: **** -109: Invariant Violation -109: nonsense -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F280D72EDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000562977F891FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000562977F866A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F280CA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000562977F867D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -109: [02:04:00] -109: -109: **** -109: Invariant Violation -109: nonsense no new line -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F280D72EDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000562977F891FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000562977F866A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F280CA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000562977F867D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 -109: **** -109: -109: [02:04:00] -109: -109: **** -109: Invariant Violation -109: nonsense with tab -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F280D72EDFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000562977F891FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000562977F866A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F280CA33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000562977F867D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: 168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 +143: [22:06:13] Rep: 0 Mol:16 +143: [22:06:13] Rep: 0 Mol:26 168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] -160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U 168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] -131/236 Test #109: testFragCatalog ........................ Passed 1.97 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch - -173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 -141: [02:04:00] Rep: 40 Mol:3 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 -141: [02:04:00] Rep: 40 Mol:7 -141: [02:04:00] Rep: 40 Mol:11 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 -141: [02:04:00] Rep: 40 Mol:15 -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:04:00] Rep: 40 Mol:19 -141: [02:04:00] Rep: 40 Mol:23 -141: [02:04:00] Rep: 40 Mol:27 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -141: [02:04:00] Rep: 40 Mol:31 -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 -141: [02:04:00] Rep: 20 Mol:1 -141: [02:04:00] Rep: 20 Mol:5 -141: [02:04:00] Rep: 20 Mol:9 -141: [02:04:00] Rep: 20 Mol:13 -141: [02:04:00] Rep: 20 Mol:17 -161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U -161: Done -161: ----------------- Test 2: some examples that caused problems in testing +143: [22:06:13] Rep: 0 Mol:21 +143: [22:06:13] Rep: 0 Mol:20 +143: [22:06:13] Rep: 0 Mol:30 +89: [22:06:13] Explicit valence for atom # 10 Si, 6, is greater than permitted 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -28827,21 +28681,12 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.011467 seconds +168: Time elapsed 0.008837 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 -132/236 Test #154: pyChemicalFeatures ..................... Passed 0.82 sec -test 174 - Start 174: testSynthonSpaceRascalSearch - -174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch -174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -174: Test timeout computed to be: 1500 -141: [02:04:00] Rep: 20 Mol:21 -141: [02:04:00] Rep: 20 Mol:25 -141: [02:04:00] Rep: 20 Mol:29 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 +143: [22:06:13] Rep: 0 Mol:25 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] @@ -28852,16 +28697,15 @@ 168: 6: PASSED. matchedRefRes = 10 168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 -161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case. +143: [22:06:13] Rep: 0 Mol:24 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -28870,8 +28714,8 @@ 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +143: [22:06:13] Rep: 0 Mol:29 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -28881,7 +28725,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.001241 seconds +168: Time elapsed 0.001458 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -28896,8 +28740,12 @@ 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 168: 7: PASSED. matchedRefRes = 7 -161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() +143: [22:06:13] Rep: 0 Mol:28 +166: Randomness seeded to: 3614120722 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +130/236 Test #166: molHashCatchTest ....................... Passed 0.19 sec 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -28905,10 +28753,9 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.012715 seconds +168: Time elapsed 0.005571 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] @@ -28923,22 +28770,16 @@ 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -161: 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 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 40 Mol:0 -141: [02:04:00] Rep: 40 Mol:4 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 40 Mol:8 -141: [02:04:00] Rep: 40 Mol:12 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] @@ -28947,77 +28788,41 @@ 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:04:00] Rep: 40 Mol:16 -141: [02:04:00] Rep: 40 Mol:20 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -141: [02:04:00] Rep: 40 Mol:24 -161: 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 -161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl -161: 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 -141: [02:04:00] Rep: 40 Mol:28 -108: .[02:04:00] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [02:04:00] SMILES Parse Error: check for mistakes around position 1: -108: [02:04:00] mydoghasfleas -108: [02:04:00] ^ -108: [02:04:00] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.014325 seconds +168: Time elapsed 0.007935 seconds 168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 168: 2: NOREF. Reference data NOT LISTED in test case. -69: [02:04:00] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [02:04:00] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 168: 3: NOREF. Reference data NOT LISTED in test case. -161: 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 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 168: 4: NOREF. Reference data NOT LISTED in test case. -117: =>start test morse custom -117: [02:04:00] test on : 365 molecules done 168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 168: 7: NOREF. Reference data NOT LISTED in test case. -89: [02:04:00] Explicit valence for atom # 3 Al, 6, is greater than permitted -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U 168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 168: 8: NOREF. Reference data NOT LISTED in test case. -143: [02:04:00] Rep: 100 Mol:3 168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 168: 9: NOREF. Reference data NOT LISTED in test case. -162: ...[02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. -143: [02:04:00] Rep: 100 Mol:7 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -143: [02:04:00] Rep: 100 Mol:11 -143: [02:04:00] Rep: 100 Mol:15 -143: [02:04:00] Rep: 100 Mol:19 -143: [02:04:00] Rep: 100 Mol:23 -143: [02:04:00] Rep: 100 Mol:27 -143: [02:04:00] Rep: 100 Mol:31 -161: Done -161: ----------------- Test 3: test reactant highlighting 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 @@ -29032,54 +28837,164 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -133/236 Test #168: testMMPA ............................... Passed 0.37 sec -40: [02:04:00] done: 500000 -40: [02:04:00] Done -test 175 - Start 175: testCIPLabeler +130: [22:06:13] done +130: [22:06:13] ------------------------------------- +130: [22:06:13] Test GitHub Issue #6958 +130: [22:06:13] DEPRECATION WARNING: please use AtomPairGenerator +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [22:06:13] Rep: 0 Mol:2 +141: [22:06:13] Rep: 0 Mol:3 +141: [22:06:13] Rep: 0 Mol:1 +141: [22:06:13] Rep: 0 Mol:0 +141: [22:06:13] Rep: 0 Mol:5 +141: [22:06:13] Rep: 0 Mol:9 +141: [22:06:13] Rep: 0 Mol:4 +141: [22:06:13] Rep: 0 Mol:13 +141: [22:06:13] Rep: 0 Mol:17 +141: [22:06:13] Rep: 0 Mol:6 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.036s +158: +158: OK +test 170 + Start 170: testRascalMCES -175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler -175: Test timeout computed to be: 1500 -130: [02:04:00] done -130: [02:04:00] ------------------------------------- -130: [02:04:00] Test GitHub Issue #6958 -130: [02:04:00] DEPRECATION WARNING: please use AtomPairGenerator -134/236 Test #130: testFingerprintGenerators .............. Passed 1.72 sec -test 176 - Start 176: pyCIPLabelsWrapTest +170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +170: Test timeout computed to be: 1500 +131/236 Test #130: testFingerprintGenerators .............. Passed 2.11 sec +132/236 Test #168: testMMPA ............................... Passed 0.27 sec +141: [22:06:13] Rep: 0 Mol:10 +141: [22:06:13] Rep: 0 Mol:8 +test 171 + Start 171: testRascalCluster -176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" -176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -176: Test timeout computed to be: 1500 -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [02:04:00] Rep: 60 Mol:3 -141: [02:04:00] Rep: 60 Mol:7 -161: Done -161: ----------------- Test 4: some examples from SMARTS in testing -141: [02:04:00] Rep: 60 Mol:11 -161: draw! -160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [02:04:00] Rep: 60 Mol:15 -141: [02:04:00] Rep: 60 Mol:19 -141: [02:04:00] Rep: 60 Mol:23 -141: [02:04:00] Rep: 60 Mol:27 -141: [02:04:00] Rep: 60 Mol:31 -69: [02:04:00] Empty atom list: 'M ALS 1 0 F' on line 8. -148: .[02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -69: de_DE.UTF-8 -69: [02:04:00] ------------------------------------- -69: [02:04:00] Test multithreading Locale Switching -126: Warning: Atom Count for residue LYS80A does not match expected count -160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U -89: [02:04:00] Explicit valence for atom # 4 Al, 6, is greater than permitted -162: ..........[02:04:00] +171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +171: Test timeout computed to be: 1500 +test 172 + Start 172: pyRascalMCES + +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +172: Test timeout computed to be: 1500 +141: [22:06:13] Rep: 0 Mol:7 +141: [22:06:13] Rep: 0 Mol:11 +141: [22:06:13] Rep: 0 Mol:21 +141: [22:06:13] Rep: 0 Mol:15 +141: [22:06:13] Rep: 0 Mol:12 +141: [22:06:13] Rep: 0 Mol:25 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue ARG64A does not match expected count +159: file test5_2.png gave hash 2649140411U not the expected 97265124U +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +141: [22:06:13] Rep: 0 Mol:19 +159: file test5_3.png gave hash 2951986966U not the expected 606188176U +159: Done +159: ----------------- Test 6 (atom labels) +148: .[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:29 +141: [22:06:13] Rep: 0 Mol:16 +141: [22:06:13] Rep: 0 Mol:23 +141: [22:06:13] Rep: 0 Mol:27 +162: ...[22:06:13] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [22:06:13] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +154: .[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:31 +160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U +159: Done +159: ----------------- Test 7 (backgrounds) +161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +159: file test7_1.png gave hash 2406197059U not the expected 1322246680U +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:20 +133/236 Test #158: pyMolCatalog ........................... Passed 0.64 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:14 +89: [22:06:13] Explicit valence for atom # 2 O, 4, is greater than permitted +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +89: [22:06:13] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [22:06:13] Explicit valence for atom # 3 Be, 4, is greater than permitted +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:24 +141: [22:06:13] Rep: 0 Mol:18 +141: [22:06:13] Rep: 0 Mol:28 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:22 +89: [22:06:13] Explicit valence for atom # 27 P, 6, is greater than permitted +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:26 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:13] Rep: 0 Mol:30 +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:13] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +159: file test7_2.png gave hash 4033628357U not the expected 1499012715U +159: Done +159: ----------------- Test8: PrepareMolDrawing +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +159: Done +159: ----------------- Test multi-threaded drawing +159: reading molecules +134/236 Test #89: multithreadedSupplierCatchTest ......... Passed 3.33 sec +test 174 + Start 174: testSynthonSpaceRascalSearch + +174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch +174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +174: Test timeout computed to be: 1500 +162: ..........[22:06:14] 162: 162: **** 162: Pre-condition Violation @@ -29093,7 +29008,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x00007FECD56DF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x00007FA7541B862C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -29104,17 +29019,17 @@ 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x00007FECD3DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x00007FECD3DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x00007FECD3DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x00007FECD3DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x00007FECD3DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x00007FA752DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x00007FA752DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x00007FA752DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x00007FA752DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x00007FA752DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x00007FECD56DC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x00007FA7541B53C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -29146,159 +29061,275 @@ 162: 55# 0x00000000006820AE in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x00007FECD68F1CA8 in /lib/x86_64-linux-gnu/libc.so.6 +162: 58# 0x00007FA75584DCA8 in /lib/x86_64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: -175: Randomness seeded to: 2448883906 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -175: [02:04:00] non kekulizable aromatic bond being treated as bond order 1 -89: [02:04:00] Explicit valence for atom # 10 Si, 6, is greater than permitted -141: [02:04:00] Rep: 40 Mol:2 -108: ....... -108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.818s -108: -108: OK -108: (Five aromatic carbons And (Not any of Five aromatic carbons)) -108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) -108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) -108: ******************************************** -108: Testing: PAINS_A 2 -108: ******************************************** -108: Testing: PAINS_B 4 -108: ******************************************** -108: Testing: PAINS_C 8 -108: ******************************************** -108: Testing: PAINS 14 -108: (Not FilterMatcher) -108: Bar -108: Count 1 -108: ******************************************** -108: {'Cl,Br,I'} -108: 1 -108: 2 -108: running -141: [02:04:00] Rep: 40 Mol:6 -161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U -141: [02:04:00] Rep: 40 Mol:10 -141: [02:04:00] Rep: 40 Mol:14 -141: [02:04:00] Rep: 40 Mol:18 -141: [02:04:00] Rep: 40 Mol:22 -141: [02:04:00] Rep: 40 Mol:26 -141: [02:04:00] Rep: 40 Mol:30 -40: [02:04:00] Testing hanoi with a functor. -141: [02:04:00] Rep: 40 Mol:1 -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [02:04:00] Rep: 40 Mol:5 -141: [02:04:00] Rep: 40 Mol:9 -141: [02:04:00] Rep: 40 Mol:13 -141: [02:04:00] Rep: 40 Mol:17 -141: [02:04:00] Rep: 40 Mol:21 -69: [02:04:00] Test multithreading (Done) -69: [02:04:00] ------------------------------------- -141: [02:04:00] Rep: 40 Mol:25 -161: done -141: [02:04:00] Rep: 40 Mol:29 -40: [02:04:00] Done -40: [02:04:00] Testing basic partition refinement. -40: [02:04:00] Done -40: [02:04:00] Testing partition refinement with neighbors. -40: [02:04:00] Done -40: [02:04:00] testing canonicalization via tie breaking. -40: [02:04:00] Done -40: [02:04:00] testing canonicalization using the wrapper. -160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -69: *************************************** -69: *************************************** -69: [02:04:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:04:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -40: [02:04:00] Done -40: [02:04:00] testing some specific ordering problems -40: [02:04:00] Finished -40: [02:04:00] testing chiral invariants. -40: [02:04:00] Finished -40: [02:04:00] testing unique ranks in w.r.t. renumbering. -160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -69: [02:04:00] bond with order 0 found on line 7. This is not part of the MDL specification. -161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U -160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U -135/236 Test #108: pyFilterCatalog ........................ Passed 2.48 sec +161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 20 Mol:1 +141: [22:06:14] Rep: 20 Mol:5 +141: [22:06:14] Rep: 20 Mol:9 +141: [22:06:14] Rep: 20 Mol:13 +141: [22:06:14] Rep: 20 Mol:17 +141: [22:06:14] Rep: 20 Mol:21 +141: [22:06:14] Rep: 20 Mol:25 +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.016s +167: +167: OK +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 20 Mol:29 +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +135/236 Test #167: pyMolHash .............................. Passed 0.58 sec +test 175 + Start 175: testCIPLabeler + +175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler +175: Test timeout computed to be: 1500 +159: generating reference drawings +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +175: Randomness seeded to: 1507447904 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +175: [22:06:14] non kekulizable aromatic bond being treated as bond order 1 +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: ..[22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[22:06:14] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [22:06:14] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.379s +154: +154: OK +141: [22:06:14] Rep: 20 Mol:3 +141: [22:06:14] Rep: 20 Mol:7 +141: [22:06:14] Rep: 20 Mol:11 +141: [22:06:14] Rep: 20 Mol:15 +141: [22:06:14] Rep: 20 Mol:19 +141: [22:06:14] Rep: 20 Mol:23 +141: [22:06:14] Rep: 20 Mol:27 +141: [22:06:14] Rep: 20 Mol:31 +161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U +141: [22:06:14] Rep: 20 Mol:0 +141: [22:06:14] Rep: 20 Mol:4 +141: [22:06:14] Rep: 20 Mol:8 +141: [22:06:14] Rep: 20 Mol:12 +141: [22:06:14] Rep: 20 Mol:16 +141: [22:06:14] Rep: 20 Mol:20 +141: [22:06:14] Rep: 40 Mol:1 +141: [22:06:14] Rep: 40 Mol:5 +141: [22:06:14] Rep: 40 Mol:9 +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.635s +156: +156: OK +156: Testing Shape Helpers wrapper +141: [22:06:14] Rep: 40 Mol:13 +141: [22:06:14] Rep: 40 Mol:17 +141: [22:06:14] Rep: 40 Mol:21 +141: [22:06:14] Rep: 40 Mol:25 +141: [22:06:14] Rep: 40 Mol:29 +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 20 Mol:24 +141: [22:06:14] Rep: 20 Mol:28 +160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U +161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U +161: Done +161: ----------------- Test 2: some examples that caused problems in testing +126: Warning: Atom Count for residue LYS80A does not match expected count +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +136/236 Test #156: pyShapeHelpers ......................... Passed 1.36 sec +test 176 + Start 176: pyCIPLabelsWrapTest + +176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" +176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +176: Test timeout computed to be: 1500 +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 0.582s +162: +162: OK +162: json lasso +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +143: [22:06:14] Rep: 100 Mol:3 +143: [22:06:14] Rep: 100 Mol:7 +143: [22:06:14] Rep: 100 Mol:11 +143: [22:06:14] Rep: 100 Mol:15 +143: [22:06:14] Rep: 100 Mol:19 +143: [22:06:14] Rep: 100 Mol:23 +143: [22:06:14] Rep: 100 Mol:27 +143: [22:06:14] Rep: 100 Mol:31 +137/236 Test #154: pyChemicalFeatures ..................... Passed 1.45 sec test 177 Start 177: pyCIPLabelsValidation 177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 177: Test timeout computed to be: 1500 -161: Done -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -136/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.99 sec +160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U +175: [22:06:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [22:06:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U +175: =============================================================================== +175: All tests passed (6577 assertions in 19 test cases) +175: +138/236 Test #175: testCIPLabeler ......................... Passed 0.40 sec +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 40 Mol:3 +160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U test 178 Start 178: deprotectTest 178: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 178: Test timeout computed to be: 1500 -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [02:04:00] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:00] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -69: [02:04:00] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [02:04:00] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [02:04:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -141: [02:04:00] Rep: 60 Mol:0 -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.048s -167: -167: OK -141: [02:04:00] Rep: 60 Mol:4 -141: [02:04:00] Rep: 60 Mol:8 -141: [02:04:00] Rep: 60 Mol:12 -141: [02:04:00] Rep: 60 Mol:16 -141: [02:04:00] Rep: 60 Mol:20 -160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U -175: [02:04:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [02:04:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: generating smiles -141: [02:04:00] Rep: 60 Mol:24 -89: [02:04:00] Explicit valence for atom # 2 O, 4, is greater than permitted -141: [02:04:00] Rep: 60 Mol:28 -69: 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 -69: converting back -89: [02:04:00] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [02:04:00] Explicit valence for atom # 3 Al, 6, is greater than permitted -143: [02:04:00] Rep: 100 Mol:1 -143: [02:04:00] Rep: 100 Mol:5 -143: [02:04:00] Rep: 100 Mol:9 -143: [02:04:00] Rep: 100 Mol:13 -143: [02:04:00] Rep: 100 Mol:17 -143: [02:04:00] Rep: 100 Mol:21 -143: [02:04:00] Rep: 100 Mol:25 -143: [02:04:00] Rep: 100 Mol:29 -141: [02:04:00] Rep: 80 Mol:3 -69: check isomorphism -141: [02:04:00] Rep: 80 Mol:7 +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 40 Mol:7 +141: [22:06:14] Rep: 40 Mol:11 +141: [22:06:14] Rep: 40 Mol:15 +141: [22:06:14] Rep: 40 Mol:19 +141: [22:06:14] Rep: 40 Mol:23 +141: [22:06:14] Rep: 40 Mol:27 +141: [22:06:14] Rep: 40 Mol:31 +161: 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 +139/236 Test #162: pyMolDraw2D ............................ Passed 1.23 sec +test 179 + Start 179: pyDeprotect + +179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" +179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap +179: Test timeout computed to be: 1500 +160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U +141: [22:06:14] Rep: 20 Mol:2 +141: [22:06:14] Rep: 20 Mol:6 +141: [22:06:14] Rep: 20 Mol:10 +161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U +141: [22:06:14] Rep: 20 Mol:14 +141: [22:06:14] Rep: 20 Mol:18 +141: [22:06:14] Rep: 20 Mol:22 +141: [22:06:14] Rep: 20 Mol:26 +141: [22:06:14] Rep: 20 Mol:30 +161: 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 +141: [22:06:14] Rep: 60 Mol:1 +141: [22:06:14] Rep: 60 Mol:5 +141: [22:06:14] Rep: 60 Mol:9 +141: [22:06:14] Rep: 60 Mol:13 +141: [22:06:14] Rep: 60 Mol:17 +141: [22:06:14] Rep: 60 Mol:21 +141: [22:06:14] Rep: 60 Mol:25 +141: [22:06:14] Rep: 60 Mol:29 +161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: 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 +161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl +161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +125: Warning: Atom Count for residue GLU150A does not match expected count +160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U +117: =>start test morse custom +117: [22:06:14] test on : 365 molecules done +178: Randomness seeded to: 1458631525 +178: =============================================================================== +178: All tests passed (111 assertions in 3 test cases) +178: +140/236 Test #178: deprotectTest .......................... Passed 0.19 sec +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U +test 180 + Start 180: testReducedGraphs + +180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs +180: Test timeout computed to be: 1500 +161: 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 +141: [22:06:14] Rep: 40 Mol:0 +141: [22:06:14] Rep: 40 Mol:4 +141: [22:06:14] Rep: 40 Mol:8 +141: [22:06:14] Rep: 40 Mol:12 +141: [22:06:14] Rep: 40 Mol:16 +141: [22:06:14] Rep: 40 Mol:20 +141: [22:06:14] Rep: 40 Mol:24 +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:14] Rep: 40 Mol:28 +180: 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, ] +180: +180: 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, ] +180: +180: 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, ] +180: +180: 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, 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+180: +180: 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, ] +180: +180: 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, ] +180: +125: Warning: Atom Count for residue ASN157A does not match expected count +180: 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, ] +180: +141/236 Test #180: testReducedGraphs ...................... Passed 0.06 sec +176: .... +176: ---------------------------------------------------------------------- +176: Ran 4 tests in 0.038s +176: +176: OK +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +160: [22:06:14] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:14] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [22:06:14] Rep: 80 Mol:1 +141: [22:06:14] Rep: 80 Mol:5 +141: [22:06:14] Rep: 80 Mol:9 +141: [22:06:14] Rep: 80 Mol:13 +141: [22:06:14] Rep: 80 Mol:17 +141: [22:06:14] Rep: 80 Mol:21 +141: [22:06:14] Rep: 80 Mol:25 +141: [22:06:14] Rep: 80 Mol:29 +141: [22:06:14] Rep: 60 Mol:3 +141: [22:06:14] Rep: 60 Mol:7 +141: [22:06:14] Rep: 60 Mol:11 +141: [22:06:14] Rep: 60 Mol:15 +141: [22:06:14] Rep: 60 Mol:19 +141: [22:06:14] Rep: 60 Mol:23 +141: [22:06:14] Rep: 60 Mol:27 +141: [22:06:14] Rep: 60 Mol:31 +122: =>start test GETAWAY +122: [22:06:14] test on : 365 molecules done 98: . 98: ---------------------------------------------------------------------- -98: Ran 11 tests in 2.227s +98: Ran 11 tests in 3.161s 98: 98: OK -141: [02:04:00] Rep: 80 Mol:11 98: True 98: == CartesianProductStrategy CartesianProductStrategy 98: 197 out of 300 @@ -29309,195 +29340,112 @@ 98: 0 10 out of 10 98: 1 5 out of 5 98: 2 6 out of 6 -98: Skipped 10000000 in 0.08978605270385742 seconds -98: Skipped 10000000 in 1.0046064853668213 seconds -98: Skipped 10000000 in 0.5606105327606201 seconds -141: [02:04:00] Rep: 80 Mol:15 -141: [02:04:00] Rep: 80 Mol:19 -141: [02:04:00] Rep: 80 Mol:23 -141: [02:04:00] Rep: 80 Mol:27 -141: [02:04:00] Rep: 80 Mol:31 -89: [02:04:00] Explicit valence for atom # 27 P, 6, is greater than permitted -148: [02:04:00] Molecule does not have explicit Hs. Consider calling AddHs() -178: Randomness seeded to: 2340345956 -178: =============================================================================== -178: All tests passed (111 assertions in 3 test cases) -178: -40: [02:04:00] Finished -40: [02:04:00] testing mol fragments. -40: [02:04:00] Finished -40: [02:04:00] testing protein round-tripping. -137/236 Test #178: deprotectTest .......................... Passed 0.11 sec -test 179 - Start 179: pyDeprotect - -179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" -179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap -179: Test timeout computed to be: 1500 -175: =============================================================================== -175: All tests passed (6577 assertions in 19 test cases) -175: -138/236 Test #175: testCIPLabeler ......................... Passed 0.42 sec -test 180 - Start 180: testReducedGraphs - -180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs -180: Test timeout computed to be: 1500 -139/236 Test #98: pyChemReactionEnumerations ............. Passed 2.70 sec +98: Skipped 10000000 in 0.20351076126098633 seconds +98: Skipped 10000000 in 1.373687505722046 seconds +98: Skipped 10000000 in 0.8665800094604492 seconds +161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U test 181 Start 181: pyReducedGraphs 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 181: Test timeout computed to be: 1500 -143: [02:04:00] Rep: 100 Mol:0 -143: [02:04:00] Rep: 100 Mol:4 -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.540s -162: -162: OK -162: json lasso -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -140/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.79 sec +142/236 Test #122: testGETAWAY ............................ Passed 3.54 sec +143/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.63 sec +148: [22:06:14] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +160: [22:06:14] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:14] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +161: Done +161: ----------------- Test 3: test reactant highlighting test 182 Start 182: trajectoryTest 182: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 182: Test timeout computed to be: 1500 -143: [02:04:00] Rep: 100 Mol:8 -143: [02:04:00] Rep: 100 Mol:12 -143: [02:04:00] Rep: 100 Mol:16 -143: [02:04:00] Rep: 100 Mol:20 -143: [02:04:00] Rep: 100 Mol:24 -143: [02:04:00] Rep: 100 Mol:28 -141/236 Test #167: pyMolHash .............................. Passed 0.85 sec test 183 Start 183: substructLibraryTest 183: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 -141: [02:04:00] Rep: 60 Mol:1 -141: [02:04:00] Rep: 60 Mol:5 -141: [02:04:00] Rep: 60 Mol:9 -141: [02:04:00] Rep: 60 Mol:13 -141: [02:04:00] Rep: 60 Mol:17 -172: ..........[02:04:00] Too many matching bond pairs (1032) so can't continue. -180: 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, 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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, ] -180: -180: 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, ] -180: -141: [02:04:00] Rep: 60 Mol:21 -141: [02:04:01] Rep: 60 Mol:25 -141: [02:04:01] Rep: 60 Mol:29 -180: 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, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] -180: -180: 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, 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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, ] -180: -180: 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, ] -180: -183: [02:04:01] ------------------------------------- -183: [02:04:01] Test1 -180: 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, ] -180: -142/236 Test #180: testReducedGraphs ...................... Passed 0.10 sec +148: [22:06:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:15] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:15] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U +161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U +143: [22:06:15] Rep: 100 Mol:1 +143: [22:06:15] Rep: 100 Mol:5 +143: [22:06:15] Rep: 100 Mol:9 +143: [22:06:15] Rep: 100 Mol:13 +143: [22:06:15] Rep: 100 Mol:17 +143: [22:06:15] Rep: 100 Mol:21 +143: [22:06:15] Rep: 100 Mol:25 +143: [22:06:15] Rep: 100 Mol:29 +143: [22:06:15] Rep: 100 Mol:0 +143: [22:06:15] Rep: 100 Mol:4 +143: [22:06:15] Rep: 100 Mol:8 +143: [22:06:15] Rep: 100 Mol:12 +143: [22:06:15] Rep: 100 Mol:16 +143: [22:06:15] Rep: 100 Mol:20 +143: [22:06:15] Rep: 100 Mol:24 +143: [22:06:15] Rep: 100 Mol:28 +172: ..........[22:06:15] Too many matching bond pairs (1032) so can't continue. +144/236 Test #98: pyChemReactionEnumerations ............. Passed 4.35 sec +141: [22:06:15] Rep: 40 Mol:2 test 184 Start 184: substructLibraryCatchTest 184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 184: Test timeout computed to be: 1500 -143/236 Test #162: pyMolDraw2D ............................ Passed 1.23 sec -test 185 - Start 185: pySubstructLibrary - -185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -185: Test timeout computed to be: 1500 -141: [02:04:01] Rep: 60 Mol:2 -141: [02:04:01] Rep: 60 Mol:6 -141: [02:04:01] Rep: 60 Mol:10 -141: [02:04:01] Rep: 60 Mol:14 -141: [02:04:01] Rep: 60 Mol:18 -141: [02:04:01] Rep: 60 Mol:22 -141: [02:04:01] Rep: 60 Mol:26 -141: [02:04:01] Rep: 60 Mol:30 -148: [02:04:01] Molecule does not have explicit Hs. Consider calling AddHs() -176: .... -176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.033s -176: -176: OK -141: [02:04:01] Rep: 80 Mol:1 -141: [02:04:01] Rep: 80 Mol:5 -141: [02:04:01] Rep: 80 Mol:9 -141: [02:04:01] Rep: 80 Mol:13 -144/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.83 sec -141: [02:04:01] Rep: 80 Mol:17 -test 186 - Start 186: testRGroupDecomp - -186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -186: Test timeout computed to be: 1500 -141: [02:04:01] Rep: 80 Mol:21 -141: [02:04:01] Rep: 80 Mol:25 -141: [02:04:01] Rep: 80 Mol:29 -141: [02:04:01] Rep: 80 Mol:0 -141: [02:04:01] Rep: 80 Mol:4 -141: [02:04:01] Rep: 80 Mol:8 -141: [02:04:01] Rep: 80 Mol:12 -141: [02:04:01] Rep: 80 Mol:16 -141: [02:04:01] Rep: 80 Mol:20 -141: [02:04:01] Rep: 80 Mol:24 -141: [02:04:01] Rep: 80 Mol:28 -145/236 Test #182: trajectoryTest ......................... Passed 0.44 sec -test 187 - Start 187: testRGroupDecompInternals - -187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -187: Test timeout computed to be: 1500 -143: [02:04:01] Rep: 100 Mol:2 -143: [02:04:01] Rep: 100 Mol:6 -143: [02:04:01] Rep: 100 Mol:10 -143: [02:04:01] Rep: 100 Mol:14 -143: [02:04:01] Rep: 100 Mol:18 -143: [02:04:01] Rep: 100 Mol:22 -143: [02:04:01] Rep: 100 Mol:26 -143: [02:04:01] Rep: 100 Mol:30 -148: [02:04:01] Molecule does not have explicit Hs. Consider calling AddHs() -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -181: ..... -181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.016s -181: -181: OK -117: =>start test AUTOCORR3D custom -117: [02:04:01] test on : 365 molecules done -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -146/236 Test #181: pyReducedGraphs ........................ Passed 0.62 sec -test 188 - Start 188: rgroupCatchTests - -188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -188: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU150A does not match expected count +141: [22:06:15] Rep: 40 Mol:6 +141: [22:06:15] Rep: 40 Mol:10 +141: [22:06:15] Rep: 40 Mol:14 +141: [22:06:15] Rep: 40 Mol:18 +161: Done +161: ----------------- Test 4: some examples from SMARTS in testing +161: draw! +148: .[22:06:15] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:15] Rep: 40 Mol:22 +141: [22:06:15] Rep: 40 Mol:26 +141: [22:06:15] Rep: 40 Mol:30 +183: [22:06:15] ------------------------------------- +183: [22:06:15] Test1 +141: [22:06:15] Rep: 60 Mol:0 +141: [22:06:15] Rep: 60 Mol:4 +141: [22:06:15] Rep: 60 Mol:8 +141: [22:06:15] Rep: 60 Mol:12 +141: [22:06:15] Rep: 60 Mol:16 +141: [22:06:15] Rep: 60 Mol:20 +141: [22:06:15] Rep: 60 Mol:24 +141: [22:06:15] Rep: 60 Mol:28 +141: [22:06:15] Rep: 80 Mol:3 +141: [22:06:15] Rep: 80 Mol:7 +141: [22:06:15] Rep: 80 Mol:11 +141: [22:06:15] Rep: 80 Mol:15 +141: [22:06:15] Rep: 80 Mol:19 +141: [22:06:15] Rep: 80 Mol:23 +141: [22:06:15] Rep: 80 Mol:27 +141: [22:06:15] Rep: 80 Mol:31 +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +143: [22:06:15] Rep: 100 Mol:2 +143: [22:06:15] Rep: 100 Mol:6 +143: [22:06:15] Rep: 100 Mol:10 +143: [22:06:15] Rep: 100 Mol:14 +143: [22:06:15] Rep: 100 Mol:18 +143: [22:06:15] Rep: 100 Mol:22 +143: [22:06:15] Rep: 100 Mol:26 +143: [22:06:15] Rep: 100 Mol:30 +160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.110s +179: Ran 5 tests in 0.133s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -29550,102 +29498,397 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -147/236 Test #187: testRGroupDecompInternals .............. Passed 0.18 sec +181: ..... +181: ---------------------------------------------------------------------- +181: Ran 5 tests in 0.018s +181: +181: OK +147: [22:06:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +145/236 Test #179: pyDeprotect ............................ Passed 1.11 sec +test 185 + Start 185: pySubstructLibrary + +185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +185: Test timeout computed to be: 1500 +146/236 Test #181: pyReducedGraphs ........................ Passed 0.77 sec +test 186 + Start 186: testRGroupDecomp + +186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +186: Test timeout computed to be: 1500 +160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U +161: done +147/236 Test #182: trajectoryTest ......................... Passed 0.76 sec +40: [22:06:15] done: 500000 +40: [22:06:15] Done +test 187 + Start 187: testRGroupDecompInternals + +187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +187: Test timeout computed to be: 1500 +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U +160: [22:06:15] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:15] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [22:06:15] Molecule does not have explicit Hs. Consider calling AddHs() +141: [22:06:15] Rep: 80 Mol:0 +160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U +141: [22:06:15] Rep: 80 Mol:4 +141: [22:06:15] Rep: 80 Mol:8 +141: [22:06:15] Rep: 80 Mol:12 +141: [22:06:15] Rep: 80 Mol:16 +141: [22:06:15] Rep: 80 Mol:20 +141: [22:06:15] Rep: 80 Mol:24 +141: [22:06:15] Rep: 80 Mol:28 +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [22:06:15] WARNING: not removing hydrogen atom with dummy atom neighbors +148/236 Test #187: testRGroupDecompInternals .............. Passed 0.08 sec +147: [22:06:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +141: [22:06:15] Rep: 60 Mol:2 +141: [22:06:15] Rep: 60 Mol:6 +141: [22:06:15] Rep: 60 Mol:10 +141: [22:06:15] Rep: 60 Mol:14 +141: [22:06:15] Rep: 60 Mol:18 +141: [22:06:15] Rep: 60 Mol:22 +141: [22:06:15] Rep: 60 Mol:26 +141: [22:06:15] Rep: 60 Mol:30 +40: [22:06:15] Testing hanoi with a functor. +40: [22:06:15] Done +40: [22:06:15] Testing basic partition refinement. +40: [22:06:15] Done +40: [22:06:15] Testing partition refinement with neighbors. +40: [22:06:15] Done +40: [22:06:15] testing canonicalization via tie breaking. +40: [22:06:15] Done +40: [22:06:15] testing canonicalization using the wrapper. +40: [22:06:15] Done +40: [22:06:15] testing some specific ordering problems +40: [22:06:15] Finished +40: [22:06:15] testing chiral invariants. +40: [22:06:15] Finished +40: [22:06:15] testing unique ranks in w.r.t. renumbering. +69: [22:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [22:06:15] deprecated group abbreviation ignored on line 24 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [22:06:15] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007F34362C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007F34362D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007F34362D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000564E41090C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000564E410F7372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000564E410779A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007F3435833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x0000564E41077AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +test 188 + Start 188: rgroupCatchTests + +188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +188: Test timeout computed to be: 1500 +147: [22:06:15] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U +183: [22:06:16] done +161: Done +149/236 Test #161: moldraw2DRxnTest1 ...................... Passed 2.73 sec test 189 Start 189: pyRGroupDecomposition 189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 189: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue ASN157A does not match expected count -184: Randomness seeded to: 3768233129 +183: [22:06:16] ------------------------------------- +183: [22:06:16] Test2 +126: Warning: Atom Count for residue GLU150A does not match expected count +117: =>start test AUTOCORR3D custom +117: [22:06:16] test on : 365 molecules done +151: 5085536345 +147: [22:06:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [22:06:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +186: [22:06:18] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +147: [22:06:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +186: [22:06:18] WARNING: not removing hydrogen atom with dummy atom neighbors +126: Warning: Atom Count for residue ASN157A does not match expected count +40: [22:06:18] Finished +40: [22:06:18] testing mol fragments. +40: [22:06:18] Finished +40: [22:06:18] testing protein round-tripping. +69: [22:06:18] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [22:06:18] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +141: [22:06:18] Rep: 80 Mol:2 +141: [22:06:18] Rep: 80 Mol:6 +141: [22:06:18] Rep: 80 Mol:10 +141: [22:06:18] Rep: 80 Mol:14 +141: [22:06:18] Rep: 80 Mol:18 +141: [22:06:18] Rep: 80 Mol:22 +141: [22:06:18] Rep: 80 Mol:26 +141: [22:06:18] Rep: 80 Mol:30 +141: [22:06:18] done +141: [22:06:18] ------------------------------------- +141: [22:06:18] Test MMFF multithreading2 +148: [22:06:18] Molecule does not have explicit Hs. Consider calling AddHs() +183: [22:06:18] done +69: ---------------------------------- +69: ---------------------------------- +69: [22:06:18] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x0000564E4109DFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000564E410F73EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000564E410779A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007F3435833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x0000564E41077AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [22:06:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +183: [22:06:18] ------------------------------------- +183: [22:06:18] Test3 (stereo options) +143: [22:06:19] done +143: [22:06:19] ------------------------------------- +143: [22:06:19] Test UFF multithreading2 +146: [22:06:12] --------------------------------- +146: [22:06:12] test3 +146: +146: [22:06:12] --------------------------------- +146: [22:06:12] test4 +146: +146: [22:06:12] --------------------------------- +146: [22:06:12] test5 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] test6 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] test15Dists +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] test Issue 215 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testMultipleConfs +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testMultipleConfsExpTors +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue227 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue236 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testOrdering +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue244 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue251 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue276 +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue284 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue285 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testIssue355 +146: +146: [22:06:18] --------------------------------- +146: [22:06:18] testRandomCoords +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 1989539 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 2091864 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test constrained embedding +146: +146: [22:06:19] ssd: 0.0752641 +183: [22:06:19] Done (stereo options) +183: [22:06:19] ------------------------------------- +183: [22:06:19] Test4 (trusted smiles) +146: [22:06:19] ssd: 0.0659363 +160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U +160: [22:06:19] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:19] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +117: =>start test 2 WHIM custom +117: [22:06:19] test on : 365 molecules done +173: Randomness seeded to: 2393043111 +173: [22:06:19] Writing the enumerated file may take quite some time and result in a large file. +184: Randomness seeded to: 1641297181 184: =============================================================================== 184: All tests passed (171 assertions in 5 test cases) 184: -148/236 Test #184: substructLibraryCatchTest .............. Passed 0.62 sec -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +150/236 Test #184: substructLibraryCatchTest .............. Passed 4.08 sec +141: [22:06:19] done +141: [22:06:19] ------------------------------------- +141: [22:06:19] Test MMFF multithreading3 test 190 Start 190: molInterchangeTest1 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -29: All 191 tests passed -149/236 Test #179: pyDeprotect ............................ Passed 0.78 sec +160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U +160: [22:06:19] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [22:06:19] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 5.105s +169: +169: OK +151/236 Test #169: pyMMPA ................................. Passed 5.89 sec +190: [22:06:19] test1: basics test 191 Start 191: molInterchangeCatchTest 191: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 191: Test timeout computed to be: 1500 -190: [02:04:01] test1: basics -190: [02:04:01] done -190: [02:04:01] test2: basic writing +160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U +190: [22:06:19] done +190: [22:06:19] test2: basic writing 190: {"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":"2025.03.1","cipRanks":[0,0]}]}]} 190: {"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":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 190: {"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":"2025.03.1","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]]}]}]} 190: {"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":"2025.03.1","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]]}]}]} -190: [02:04:01] done -190: [02:04:01] test3: writing conformers +190: [22:06:19] done +190: [22:06:19] test3: writing conformers 190: {"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":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -190: [02:04:01] done -190: [02:04:01] test4: writing properties +190: [22:06:19] done +190: [22:06:19] test4: writing properties +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U 190: {"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":"2025.03.1","cipRanks":[0,0]}]}]} -190: [02:04:01] done -190: [02:04:01] test5: writing partial charges +190: [22:06:19] done +190: [22:06:19] test5: writing partial charges 190: {"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":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -190: [02:04:01] testing parse options -190: [02:04:01] done -190: [02:04:01] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +190: [22:06:19] testing parse options +190: [22:06:19] done +190: [22:06:19] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 190: {"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":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -190: [02:04:01] done -190: [02:04:01] testing 'either' stereochemistry -190: [02:04:01] done -150/236 Test #190: molInterchangeTest1 .................... Passed 0.05 sec +190: [22:06:19] done +190: [22:06:19] testing 'either' stereochemistry +190: [22:06:19] done +152/236 Test #190: molInterchangeTest1 .................... Passed 0.22 sec test 192 Start 192: pyMolInterchange 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 192: Test timeout computed to be: 1500 -183: [02:04:01] done -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -183: [02:04:01] ------------------------------------- -183: [02:04:01] Test2 -191: Randomness seeded to: 1899080588 -191: [02:04:01] unrecognized bond type 12 set to zero while writing -191: [02:04:01] unrecognized bond type 0 set to zero while writing +69: [22:06:19] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [22:06:19] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +183: [22:06:19] Done (trusted smiles) +183: [22:06:19] ------------------------------------- +183: [22:06:19] Testing C++ docs +183: [22:06:19] Done (C++ doc tests) +183: [22:06:19] ------------------------------------- +183: [22:06:19] Testing C++ ring query: PatternHolder +183: [22:06:19] Done (C++ ring query tests) +183: [22:06:19] ------------------------------------- +183: [22:06:19] Testing C++ ring query: TautomerPatternHolder +183: [22:06:19] Done (C++ ring query tests) +183: [22:06:19] ------------------------------------- +183: [22:06:19] Add Patterns +191: Randomness seeded to: 927668271 +191: [22:06:19] unrecognized bond type 12 set to zero while writing +191: [22:06:19] unrecognized bond type 0 set to zero while writing 191: =============================================================================== 191: All tests passed (125 assertions in 7 test cases) 191: -151/236 Test #191: molInterchangeCatchTest ................ Passed 0.08 sec +153/236 Test #191: molInterchangeCatchTest ................ Passed 0.13 sec +188: Randomness seeded to: 3911972525 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +148: [22:06:19] Molecule does not have explicit Hs. Consider calling AddHs() test 193 Start 193: testSLNParse 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 193: Test timeout computed to be: 1500 +154/236 Test #188: rgroupCatchTests ....................... Passed 3.70 sec +test 194 + Start 194: pySLNParse + +194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" +194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap +194: Test timeout computed to be: 1500 +69: [22:06:19] Empty atom list: 'M ALS 1 0 F' on line 8. +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +155/236 Test #69: fileParsersTest1 ....................... Passed 9.23 sec +test 195 + Start 195: pyGraphMolWrap + +195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" +195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +195: Test timeout computed to be: 1500 193: Atoms: 193: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 193: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -29659,447 +29902,119 @@ 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 -193: [02:04:01] SLN Parse Error: syntax error while parsing: CH4[I=13] -193: [02:04:01] Failed parsing SLN 'CH4[I=13]' -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -186: [02:04:01] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -141: [02:04:01] Rep: 80 Mol:2 -141: [02:04:01] Rep: 80 Mol:6 -141: [02:04:01] Rep: 80 Mol:10 -141: [02:04:01] Rep: 80 Mol:14 -193: [02:04:01] SLN Parser error: Atom ID 1 appears *after* its ring closure. -193: [02:04:01] SLN Parser error: Ring closure 1 does not have a corresponding opener. -193: [02:04:01] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -193: [02:04:01] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -193: [02:04:01] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -193: [02:04:01] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -193: [02:04:01] SLN Parse Error: syntax error while parsing: CH4 fff -193: [02:04:01] Failed parsing SLN 'CH4 fff' -193: [02:04:01] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -193: [02:04:01] Failed parsing SLN 'C[charge=+1] foo' -186: [02:04:01] WARNING: not removing hydrogen atom with dummy atom neighbors -193: [02:04:01] Query property 'is' ignored on non-query atom -193: [02:04:01] Query property 'is' ignored on non-query atom -152/236 Test #193: testSLNParse ........................... Passed 0.06 sec -test 194 - Start 194: pySLNParse - -194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" -194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap -194: Test timeout computed to be: 1500 -141: [02:04:01] Rep: 80 Mol:18 -141: [02:04:01] Rep: 80 Mol:22 -141: [02:04:01] Rep: 80 Mol:26 -141: [02:04:01] Rep: 80 Mol:30 -160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -160: [02:04:01] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:01] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U -160: [02:04:01] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [02:04:01] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -147: [02:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -146: [02:03:59] --------------------------------- -146: [02:03:59] test3 -146: -146: [02:03:59] --------------------------------- -146: [02:03:59] test4 -146: -146: [02:03:59] --------------------------------- -146: [02:03:59] test5 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test6 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test15Dists -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test Issue 215 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testMultipleConfs -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testMultipleConfsExpTors -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue227 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue236 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testOrdering -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue244 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue251 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue276 -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue284 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue285 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testIssue355 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] testRandomCoords -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test sf.net issue 1989539 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test sf.net issue 2091864 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test constrained embedding -146: -146: [02:04:01] ssd: 0.0752641 -146: [02:04:01] ssd: 0.0659363 -160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -148: [02:04:02] Molecule does not have explicit Hs. Consider calling AddHs() -183: [02:04:02] done -192: .. -192: ---------------------------------------------------------------------- -192: Ran 2 tests in 0.013s -192: -192: OK -183: [02:04:02] ------------------------------------- -183: [02:04:02] Test3 (stereo options) -153/236 Test #192: pyMolInterchange ....................... Passed 0.43 sec -test 195 - Start 195: pyGraphMolWrap - -195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" -195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -195: Test timeout computed to be: 1500 -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.011s -194: -194: OK -146: [02:04:01] --------------------------------- -146: [02:04:01] test sf.net issue 2091974 -146: -146: [02:04:01] --------------------------------- -146: [02:04:01] test sf.net issue 2835784 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test sf.net issue 3019283 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test sf.net issue 3238580 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test sf.net issue 3483968 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test github issue 55 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test1 -146: -146: [02:04:02] --------------------------------- -146: [02:04:02] test multi-threading -146: -146: building molecules -188: Randomness seeded to: 2395095649 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -154/236 Test #188: rgroupCatchTests ....................... Passed 0.63 sec -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -test 196 - Start 196: pyTestConformerWrap - -196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" -196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -196: Test timeout computed to be: 1500 -146: generating reference data -117: =>start test 2 WHIM custom -117: [02:04:02] test on : 365 molecules done -155/236 Test #194: pySLNParse ............................. Passed 0.39 sec -test 197 - Start 197: pyTestTrajectory - -197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" -197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 -183: [02:04:02] Done (stereo options) -183: [02:04:02] ------------------------------------- -183: [02:04:02] Test4 (trusted smiles) -141: [02:04:02] done -141: [02:04:02] ------------------------------------- -141: [02:04:02] Test MMFF multithreading2 -148: [02:04:02] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue GLU150A does not match expected count -40: [02:04:02] Finished -40: [02:04:02] testing stability w.r.t. renumbering. -183: [02:04:02] Done (trusted smiles) -183: [02:04:02] ------------------------------------- -183: [02:04:02] Testing C++ docs -183: [02:04:02] Done (C++ doc tests) -183: [02:04:02] ------------------------------------- -183: [02:04:02] Testing C++ ring query: PatternHolder -183: [02:04:02] Done (C++ ring query tests) -183: [02:04:02] ------------------------------------- -183: [02:04:02] Testing C++ ring query: TautomerPatternHolder -183: [02:04:02] Done (C++ ring query tests) -183: [02:04:02] ------------------------------------- -183: [02:04:02] Add Patterns -197: [02:04:02] -197: -197: **** -197: Pre-condition Violation -197: from must be < size() -197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -197: Failed Expression: from < static_cast(size()) -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 -197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so -197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# _PyObject_MakeTpCall in /usr/bin/python3 -197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 24# 0x00000000005C30D9 in /usr/bin/python3 -197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 26# 0x000000000064B89F in /usr/bin/python3 -197: 27# 0x000000000069ECA0 in /usr/bin/python3 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x00000000005C30D9 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000064B89F in /usr/bin/python3 -197: 33# 0x000000000069ECA0 in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x00000000005C30D9 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000064B89F in /usr/bin/python3 -197: 39# 0x000000000069ECA0 in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x0000000000599C8E in /usr/bin/python3 -197: 43# _PyObject_MakeTpCall in /usr/bin/python3 -197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 45# PyEval_EvalCode in /usr/bin/python3 -197: 46# 0x000000000066DA21 in /usr/bin/python3 -197: 47# 0x0000000000669A8C in /usr/bin/python3 -197: 48# 0x0000000000682973 in /usr/bin/python3 -197: 49# 0x0000000000682273 in /usr/bin/python3 -197: 50# 0x00000000006820AE in /usr/bin/python3 -197: 51# Py_RunMain in /usr/bin/python3 -197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 -197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -197: 55# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -197: .[02:04:02] -197: -197: **** -197: Pre-condition Violation -197: from must be < size() -197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp -197: Failed Expression: from < static_cast(size()) -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 -197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so -197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# _PyObject_MakeTpCall in /usr/bin/python3 -197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 24# 0x00000000005C30D9 in /usr/bin/python3 -197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 26# 0x000000000064B89F in /usr/bin/python3 -197: 27# 0x000000000069ECA0 in /usr/bin/python3 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x00000000005C30D9 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000064B89F in /usr/bin/python3 -197: 33# 0x000000000069ECA0 in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x00000000005C30D9 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000064B89F in /usr/bin/python3 -197: 39# 0x000000000069ECA0 in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x0000000000599C8E in /usr/bin/python3 -197: 43# _PyObject_MakeTpCall in /usr/bin/python3 -197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 45# PyEval_EvalCode in /usr/bin/python3 -197: 46# 0x000000000066DA21 in /usr/bin/python3 -197: 47# 0x0000000000669A8C in /usr/bin/python3 -197: 48# 0x0000000000682973 in /usr/bin/python3 -197: 49# 0x0000000000682273 in /usr/bin/python3 -197: 50# 0x00000000006820AE in /usr/bin/python3 -197: 51# Py_RunMain in /usr/bin/python3 -197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 -197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -197: 55# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -126: Warning: Atom Count for residue ASN157A does not match expected count -160: [02:04:02] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U -69: [02:04:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:04:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:04:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [02:04:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -40: [02:04:02] Finished -40: [02:04:02] testing smiles round-tripping. -69: [02:04:02] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [02:04:02] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007F5E120C8531 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007F5E120D1DFA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007F5E120D217D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x000055ABC3364C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x000055ABC33CB372 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x000055ABC334B9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007F5E11633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x000055ABC334BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -196: ...... -196: ---------------------------------------------------------------------- -196: Ran 6 tests in 0.045s -196: -196: OK +193: [22:06:19] SLN Parse Error: syntax error while parsing: CH4[I=13] +193: [22:06:19] Failed parsing SLN 'CH4[I=13]' +193: [22:06:19] SLN Parser error: Atom ID 1 appears *after* its ring closure. +193: [22:06:19] SLN Parser error: Ring closure 1 does not have a corresponding opener. +193: [22:06:19] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +193: [22:06:19] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +193: [22:06:19] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +193: [22:06:19] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +193: [22:06:19] SLN Parse Error: syntax error while parsing: CH4 fff +193: [22:06:19] Failed parsing SLN 'CH4 fff' +193: [22:06:19] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +193: [22:06:19] Failed parsing SLN 'C[charge=+1] foo' +193: [22:06:19] Query property 'is' ignored on non-query atom +193: [22:06:19] Query property 'is' ignored on non-query atom +156/236 Test #193: testSLNParse ........................... Passed 0.06 sec +151: 1250910624 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +160: [22:06:19] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U 160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U -143: [02:04:02] done -143: [02:04:02] ------------------------------------- -143: [02:04:02] Test UFF multithreading2 -141: [02:04:02] done -141: [02:04:02] ------------------------------------- -141: [02:04:02] Test MMFF multithreading3 -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 2.110s -172: -172: OK -156/236 Test #196: pyTestConformerWrap .................... Passed 0.68 sec +143: [22:06:19] done +143: [22:06:19] ------------------------------------- +143: [22:06:19] Test UFF multithreading3 +141: [22:06:19] done +141: [22:06:19] ------------------------------------- +141: [22:06:19] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [22:06:19] done +141: [22:06:19] ------------------------------------- +141: [22:06:19] Testing github 224: crash during MMFF parameterization . +141: [22:06:19] done +141: [22:06:19] ------------------------------------- +141: [22:06:19] Testing github6728: crash due to missing stretch-bend params. +test 196 + Start 196: pyTestConformerWrap + +196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" +196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +196: Test timeout computed to be: 1500 +157/236 Test #141: testMMFFForceFieldHelpers .............. Passed 7.75 sec +158/236 Test #151: molAlignCatchTest ...................... Passed 7.04 sec +test 197 + Start 197: pyTestTrajectory + +197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" +197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 test 198 Start 198: pyTestSGroups 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" 198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -157/236 Test #172: pyRascalMCES ........................... Passed 2.66 sec -test 199 - Start 199: pyTestThreads - -199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" -199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -199: Test timeout computed to be: 1500 -173: Randomness seeded to: 4096980563 -173: [02:04:02] Writing the enumerated file may take quite some time and result in a large file. -151: 3447197098 -69: [02:04:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [02:04:03] 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: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 2091974 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 2835784 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 3019283 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 3238580 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test sf.net issue 3483968 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test github issue 55 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test1 +146: +146: [22:06:19] --------------------------------- +146: [22:06:19] test multi-threading +146: +146: building molecules +146: generating reference data 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.000 seconds 163: 163: test32() 163: 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 -163: Time elapsed 0.133 seconds +163: Time elapsed 0.083 seconds 163: 163: test190() 163: 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 -163: Time elapsed 0.018 seconds +163: Time elapsed 0.020 seconds 163: 163: test3() 163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.031 seconds +163: Time elapsed 0.025 seconds 163: 163: testSimpleFast() 163: 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 -163: Time elapsed 0.177 seconds +163: Time elapsed 0.112 seconds 163: 163: testSimple() 163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.102 seconds +163: Time elapsed 0.215 seconds 163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.193 seconds +163: Time elapsed 0.380 seconds 163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.272 seconds +163: Time elapsed 0.205 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.020 seconds +163: Time elapsed 0.018 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.034 seconds +163: Time elapsed 0.031 seconds 163: 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 -163: Time elapsed 0.027 seconds +163: Time elapsed 0.030 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30107,11 +30022,11 @@ 163: 163: testRing1() 163: 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 -163: Time elapsed 1.072 seconds +163: Time elapsed 0.966 seconds 163: 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 -163: Time elapsed 0.536 seconds +163: Time elapsed 3.507 seconds 163: 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 -163: Time elapsed 0.549 seconds +163: Time elapsed 1.010 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30135,40 +30050,58 @@ 163: 163: testJnk1LigandsDistance() 163: 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 -163: Time elapsed 0.010 seconds +163: Time elapsed 0.022 seconds 163: 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 -117: =>start test 1 WHIM custom -117: [02:04:03] test on : 365 molecules done -141: [02:04:03] done -141: [02:04:03] ------------------------------------- -141: [02:04:03] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [02:04:03] done -141: [02:04:03] ------------------------------------- -141: [02:04:03] Testing github 224: crash during MMFF parameterization . -195: ..............[02:04:03] SMARTS Parse Error: syntax error while parsing: fiib -195: [02:04:03] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -141: [02:04:03] done -141: [02:04:03] ------------------------------------- -141: [02:04:03] Testing github6728: crash due to missing stretch-bend params. +160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U +160: [22:06:20] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +143: [22:06:20] done +143: [22:06:20] ------------------------------------- +143: [22:06:20] Testing GitHubIssue62. +143: [22:06:20] beta-lactam 39.6387 +143: [22:06:20] cyclopropanone 174.698 +143: [22:06:20] aziridine 337.986 +143: [22:06:20] aziridinone 115.248 +143: [22:06:20] isobutene 2.48217 +143: [22:06:20] acetone 1.91788 +143: [22:06:20] cyclopentanone 10.1648 +143: [22:06:20] cyclopropene 99.4921 +143: [22:06:20] cyclobutene 41.0156 +143: [22:06:20] cyclopropane 267.236 +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Issue252: Bad definitions for Crippen atom types. +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.035s +194: +194: OK +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of ChiVs. +192: .. +192: ---------------------------------------------------------------------- +192: Ran 2 tests in 0.029s +192: +192: OK 163: Time elapsed 0.002 seconds 163: 163: test18() 163: 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]1 163: 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 -163: Time elapsed 0.008 seconds +163: Time elapsed 0.007 seconds 163: 163: test504() 163: 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]1 163: 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 -163: Time elapsed 0.105 seconds +163: Time elapsed 0.098 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.001 seconds 163: 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 -163: Time elapsed 0.027 seconds +163: Time elapsed 0.028 seconds 163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0007 seconds. bond[0]=6 +163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0014 seconds. bond[0]=6 163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0007 seconds +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0014 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 @@ -30187,7 +30120,7 @@ 163: HashFoundInCache= 0 163: ExactMatchCalls = 0 163: ExactMatchFound = 0 -163: Time elapsed 0.001 seconds +163: Time elapsed 0.002 seconds 163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 @@ -30216,6 +30149,7 @@ 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 163: res sub = 1 size=4 +143: [22:06:20] gamma-lactam 15.7471 163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 163: res sub = 1 size=4 @@ -30246,7 +30180,6 @@ 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 -158/236 Test #141: testMMFFForceFieldHelpers .............. Passed 4.25 sec 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = OC(F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 @@ -30270,6 +30203,9 @@ 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of ChiNs. 163: res sub = 1 size=3 163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 @@ -30284,84 +30220,702 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of HallKierAlpha. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of Kappa1. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of Kappa2. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of Kappa3. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Crippen atom type calculations. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test ring descriptors +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test other count descriptors. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test MQN +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test GitHub Issue 56. +111: [22:06:20] WARNING: not removing hydrogen atom without neighbors +111: [22:06:20] WARNING: not removing hydrogen atom without neighbors +111: [22:06:20] WARNING: not removing hydrogen atom without neighbors +111: [22:06:20] WARNING: not removing hydrogen atom without neighbors +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github92: Bad Crippen atom type for pyrrole H. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github362: order dependence in Kier-Hall descriptors. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test calculation of spiro and bridgehead counts. +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github694: ExactMolWt ignoring the mass of the electron +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Testing Properties and KitchenSink +111: [22:06:20] ---Caught keyerror (bad property name)--- +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test USR Descriptor +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github #1973: support P and S terms for TPSA calculation +111: [22:06:20] done +111: [22:06:20] ------------------------------------- +111: [22:06:20] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [22:06:20] done +159/236 Test #111: testDescriptors ........................ Passed 9.29 sec +143: [22:06:20] trans-2,3-diphenylcyclopropan-1-one 203.398 +test 199 + Start 199: pyTestThreads + +199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" +199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +199: Test timeout computed to be: 1500 +160/236 Test #192: pyMolInterchange ....................... Passed 0.92 sec +161/236 Test #194: pySLNParse ............................. Passed 0.76 sec +143: [22:06:20] cis-2,3-diphenylcyclopropan-1-one 206.852 test 200 Start 200: pyTestMultithreadedMolSupplier 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -143: [02:04:03] done -143: [02:04:03] ------------------------------------- -143: [02:04:03] Test UFF multithreading3 -195: ....[02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] Spurious data before the first property will be ignored -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] Spurious data before the first property will be ignored -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] Property will be truncated after the first blank line -195: [02:04:03] ERROR: Problems encountered parsing data fields -195: [02:04:03] ERROR: moving to the beginning of the next molecule -195: [02:04:03] Property will be truncated after the first blank line -40: [02:04:03] Finished -40: [02:04:03] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [02:04:03] Finished -195: .[02:04:03] SMILES Parse Error: syntax error while parsing: fail -195: [02:04:03] SMILES Parse Error: check for mistakes around position 1: -195: [02:04:03] fail -195: [02:04:03] ^ -195: [02:04:03] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -195: [02:04:03] ERROR: Smiles parse error on line 2 -195: [02:04:03] ERROR: Cannot create molecule from : 'fail' -195: >>> This may result in an infinite loop. It should finish almost instantly -195: <<< OK, it finished. -159/236 Test #40: hanoiTest .............................. Passed 5.61 sec test 201 Start 201: pyTestPropertyLists 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" 201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 -69: ---------------------------------- -69: ---------------------------------- -69: [02:04:03] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x000055ABC3371FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x000055ABC33CB3EA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x000055ABC334B9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007F5E11633CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x000055ABC334BAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [02:04:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -197: .[02:04:03] +40: [22:06:20] Finished +40: [22:06:20] testing stability w.r.t. renumbering. +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 5.688s +172: +172: OK +117: =>start test 1 WHIM custom +117: [22:06:20] test on : 365 molecules done +162/236 Test #42: resMolSupplierTest ..................... Passed 10.15 sec +test 202 + Start 202: pyCDXMLTest + +202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" +202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +202: Test timeout computed to be: 1500 +143: [22:06:20] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [22:06:20] cyclopropylidencyclobutane 218.879 +40: [22:06:20] Finished +40: [22:06:20] testing smiles round-tripping. +143: [22:06:20] diphenylmethylidencyclobutane 79.6139 +143: [22:06:20] done +143: [22:06:20] ------------------------------------- +143: [22:06:20] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [22:06:20] done +143: [22:06:20] ------------------------------------- +143: [22:06:20] Test square planar complexes +143: [22:06:20] done +143: [22:06:20] ------------------------------------- +143: [22:06:20] Test octahedral complexes +143: [22:06:20] done +163/236 Test #143: testUFFForceFieldHelpers ............... Passed 8.37 sec +test 203 + Start 203: molStandardizeTest + +203: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +203: Test timeout computed to be: 1500 +164/236 Test #172: pyRascalMCES ........................... Passed 6.87 sec +195: ..............[22:06:20] SMARTS Parse Error: syntax error while parsing: fiib +195: [22:06:20] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +195: ....[22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] Spurious data before the first property will be ignored +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] Spurious data before the first property will be ignored +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] Property will be truncated after the first blank line +195: [22:06:20] ERROR: Problems encountered parsing data fields +195: [22:06:20] ERROR: moving to the beginning of the next molecule +195: [22:06:20] Property will be truncated after the first blank line +195: .[22:06:20] SMILES Parse Error: syntax error while parsing: fail +195: [22:06:20] SMILES Parse Error: check for mistakes around position 1: +195: [22:06:20] fail +195: [22:06:20] ^ +195: [22:06:20] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +195: [22:06:20] ERROR: Smiles parse error on line 2 +195: [22:06:20] ERROR: Cannot create molecule from : 'fail' +195: >>> This may result in an infinite loop. It should finish almost instantly +195: <<< OK, it finished. +197: [22:06:20] +197: +197: **** +197: Pre-condition Violation +197: from must be < size() +197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +197: Failed Expression: from < static_cast(size()) +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 +197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so +197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# _PyObject_MakeTpCall in /usr/bin/python3 +197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 24# 0x00000000005C30D9 in /usr/bin/python3 +197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 26# 0x000000000064B89F in /usr/bin/python3 +197: 27# 0x000000000069ECA0 in /usr/bin/python3 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x00000000005C30D9 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000064B89F in /usr/bin/python3 +197: 33# 0x000000000069ECA0 in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x00000000005C30D9 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000064B89F in /usr/bin/python3 +197: 39# 0x000000000069ECA0 in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x0000000000599C8E in /usr/bin/python3 +197: 43# _PyObject_MakeTpCall in /usr/bin/python3 +197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 45# PyEval_EvalCode in /usr/bin/python3 +197: 46# 0x000000000066DA21 in /usr/bin/python3 +197: 47# 0x0000000000669A8C in /usr/bin/python3 +197: 48# 0x0000000000682973 in /usr/bin/python3 +197: 49# 0x0000000000682273 in /usr/bin/python3 +197: 50# 0x00000000006820AE in /usr/bin/python3 +197: 51# Py_RunMain in /usr/bin/python3 +197: 52# Py_BytesMain in /usr/bin/python3 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +197: 55# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +197: .[22:06:20] +197: +197: **** +197: Pre-condition Violation +197: from must be < size() +197: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp +197: Failed Expression: from < static_cast(size()) +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 +197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so +197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# _PyObject_MakeTpCall in /usr/bin/python3 +197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 24# 0x00000000005C30D9 in /usr/bin/python3 +197: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 26# 0x000000000064B89F in /usr/bin/python3 +197: 27# 0x000000000069ECA0 in /usr/bin/python3 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x00000000005C30D9 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000064B89F in /usr/bin/python3 +197: 33# 0x000000000069ECA0 in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x00000000005C30D9 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000064B89F in /usr/bin/python3 +197: 39# 0x000000000069ECA0 in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x0000000000599C8E in /usr/bin/python3 +197: 43# _PyObject_MakeTpCall in /usr/bin/python3 +197: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 45# PyEval_EvalCode in /usr/bin/python3 +197: 46# 0x000000000066DA21 in /usr/bin/python3 +197: 47# 0x0000000000669A8C in /usr/bin/python3 +197: 48# 0x0000000000682973 in /usr/bin/python3 +197: 49# 0x0000000000682273 in /usr/bin/python3 +197: 50# 0x00000000006820AE in /usr/bin/python3 +197: 51# Py_RunMain in /usr/bin/python3 +197: 52# Py_BytesMain in /usr/bin/python3 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +197: 55# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +148: [22:06:20] Molecule does not have explicit Hs. Consider calling AddHs() +test 204 + Start 204: molNormalizeTest + +204: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +204: Test timeout computed to be: 1500 +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.013s +202: +202: OK +204: [22:06:20] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +196: ...... +196: ---------------------------------------------------------------------- +196: Ran 6 tests in 0.048s +196: +196: OK +165/236 Test #202: pyCDXMLTest ............................ Passed 0.33 sec +201: [22:06:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [22:06:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [22:06:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: .[22:06:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [22:06:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [22:06:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: ...[22:06:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [22:06:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [22:06:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: . +201: ---------------------------------------------------------------------- +201: Ran 5 tests in 0.014s +201: +201: OK +40: [22:06:20] Finished +40: [22:06:20] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [22:06:20] Finished +test 205 + Start 205: molValidateTest + +205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +205: Test timeout computed to be: 1500 +166/236 Test #196: pyTestConformerWrap .................... Passed 1.04 sec +198: ............. +198: ---------------------------------------------------------------------- +198: Ran 13 tests in 0.073s +198: +198: OK +198: Testing SubstanceGroups wrapper +167/236 Test #40: hanoiTest .............................. Passed 10.61 sec +test 206 + Start 206: molChargeTest + +206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +206: Test timeout computed to be: 1500 +test 207 + Start 207: molTautomerTest + +207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +207: Test timeout computed to be: 1500 +195: ............[22:06:20] Explicit valence for atom # 1 C, 5, is greater than permitted +168/236 Test #201: pyTestPropertyLists .................... Passed 0.50 sec +test 208 + Start 208: molStandardizeSmallTest + +208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +208: Test timeout computed to be: 1500 +204: [22:06:20] Initializing Normalizer +204: [22:06:20] Running Normalizer +204: [22:06:20] Rule applied: BrokenazidetoN=N+=N- +204: [22:06:20] Initializing Normalizer +204: [22:06:20] Running Normalizer +204: [22:06:20] Initializing Normalizer +204: [22:06:20] Running Normalizer +169/236 Test #204: molNormalizeTest ....................... Passed 0.25 sec +test 209 + Start 209: molFragmentTest + +209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +209: Test timeout computed to be: 1500 +148: [22:06:21] Molecule does not have explicit Hs. Consider calling AddHs() +205: ERROR: [FeaturesValidation] Query atom 0 is not allowed +205: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed +205: ERROR: [FeaturesValidation] Query bond 0 is not allowed +205: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed +205: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed +205: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed +205: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed +205: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed +205: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. +205: here +205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. +205: there +205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. +170/236 Test #208: molStandardizeSmallTest ................ Passed 0.06 sec +test 210 + Start 210: molStandardizeCatchTest + +210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +210: Test timeout computed to be: 1500 +171/236 Test #205: molValidateTest ........................ Passed 0.17 sec +test 211 + Start 211: molStandardizePipelineTest + +211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +211: Test timeout computed to be: 1500 +195: ......[22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: .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)| +172/236 Test #198: pyTestSGroups .......................... Passed 1.20 sec +test 212 + Start 212: pyMolStandardize + +212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +212: Test timeout computed to be: 1500 +209: [22:06:21] SMARTS Parse Error: syntax error while parsing: [Cl +209: [22:06:21] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +173/236 Test #209: molFragmentTest ........................ Passed 0.14 sec +test 213 + Start 213: testScaffoldNetwork + +213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +213: Test timeout computed to be: 1500 +211: Randomness seeded to: 4170411016 +211: 1 Counts line too short: '' on line4 +211: 1 Could not instantiate a valid molecule from input +160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U +211: 8 Molecule has no atoms +211: [22:06:21] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [22:06:21] Explicit valence for atom # 1 N, 4, is greater than permitted +211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +211: 128 An error occurred while preparing the molecule for standardization. +160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U +211: 8 The molecule contains an unknown isotope: 3C +211: 4 Query atom 0 is not allowed +211: 4 Bond 0 of aromatic type is not allowed +211: 4 Bond 1 of aromatic type is not allowed +211: 4 Bond 2 of aromatic type is not allowed +211: 4 Bond 3 of aromatic type is not allowed +211: 4 Bond 5 of aromatic type is not allowed +211: 4 Bond 6 of aromatic type is not allowed +211: 4 Bond 2 of dative type is not allowed +211: 4 Bond 3 of dative type is not allowed +211: 4 Enhanced stereochemistry features are not allowed +211: 8 The radical at atom 0 is not allowed +211: [22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: 16 The molecule includes non-null Z coordinates +211: 32 Atom 0 too close to bond 2 +211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +195: ........[22:06:21] non-ring atom 0 marked aromatic +195: [22:06:21] non-ring atom 0 marked aromatic +195: [22:06:21] +195: +195: **** +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 10.771s +12: +12: OK +211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: [22:06:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# 0x00007F8740284A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x00000000005C30D9 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x000000000064B89F in /usr/bin/python3 +195: 33# 0x000000000069ECA0 in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x00000000005C30D9 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x000000000064B89F in /usr/bin/python3 +195: 39# 0x000000000069ECA0 in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x00000000005C30D9 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x000000000064B89F in /usr/bin/python3 +195: 45# 0x000000000069ECA0 in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x0000000000599C8E in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x000000000066DA21 in /usr/bin/python3 +195: 53# 0x0000000000669A8C in /usr/bin/python3 +195: 54# 0x0000000000682973 in /usr/bin/python3 +195: 55# 0x0000000000682273 in /usr/bin/python3 +195: 56# 0x00000000006820AE in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +174/236 Test #206: molChargeTest .......................... Passed 0.27 sec +195: [22:06:21] non-ring atom 0 marked aromatic +195: [22:06:21] non-ring atom 0 marked aromatic +195: [22:06:21] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 12 < 6 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# 0x00007F8740284A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x00000000005C30D9 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x000000000064B89F in /usr/bin/python3 +195: 33# 0x000000000069ECA0 in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x00000000005C30D9 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x000000000064B89F in /usr/bin/python3 +195: 39# 0x000000000069ECA0 in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x00000000005C30D9 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x000000000064B89F in /usr/bin/python3 +195: 45# 0x000000000069ECA0 in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x0000000000599C8E in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x000000000066DA21 in /usr/bin/python3 +195: 53# 0x0000000000669A8C in /usr/bin/python3 +195: 54# 0x0000000000682973 in /usr/bin/python3 +195: 55# 0x0000000000682273 in /usr/bin/python3 +195: 56# 0x00000000006820AE in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +195: ...............[22:06:21] 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. +195: [22:06:21] 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. +211: 16 The molecule includes non-null Z coordinates +211: 64 Atom 0 has adjacent stereo bonds with like orientation +211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 16777216 The representation of some functional groups was adjusted. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 8388608 One or more metal atoms were disconnected. +211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +211: 67108864 The protonation state was adjusted. +211: 16777216 The "wavy" style of bond 4 was removed +211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 2 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 1 was removed +211: 16777216 The "wavy" style of bond 4 was removed +211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +211: 16777216 The "wavy" style of bond 3 was removed +211: 16777216 The representation of some functional groups was adjusted. +211: [22:06:21] Can't kekulize mol. Unkekulized atoms: 2 3 5 +211: =============================================================================== +211: All tests passed (268 assertions in 5 test cases) +211: +200: .s. +200: ---------------------------------------------------------------------- +200: Ran 3 tests in 0.404s +200: +200: OK (skipped=1) +200: Testing Smiles and SD MultithreadedMolSupplier +test 214 + Start 214: pyScaffoldNetwork + +214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +214: Test timeout computed to be: 1500 +175/236 Test #12: pyBV ................................... Passed 11.17 sec +176/236 Test #211: molStandardizePipelineTest ............. Passed 0.35 sec +test 215 + Start 215: pyScaffoldNetworkPickling + +215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +215: Test timeout computed to be: 1500 +test 216 + Start 216: testMolEnumerator + +216: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator +216: Test timeout computed to be: 1500 +160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U +197: .[22:06:21] 197: 197: **** -195: ............[02:04:03] Explicit valence for atom # 1 C, 5, is greater than permitted 197: Range Error 197: snapshotNum 197: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30374,23 +30928,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 @@ -30422,13 +30976,13 @@ 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[02:04:03] +197: .[22:06:21] 197: 197: **** 197: Pre-condition Violation @@ -30442,23 +30996,23 @@ 197: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30490,16 +31044,15 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ..[02:04:03] +197: ..[22:06:21] 197: 197: **** -195: ......[02:04:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 197: Pre-condition Violation 197: The trajectory must have dimension == 3 197: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30511,23 +31064,23 @@ 197: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30559,19 +31112,15 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[02:04:03] +197: .[22:06:21] 197: 197: **** -195: [02:04:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [02:04:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [02:04:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: .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)| 197: Pre-condition Violation 197: d_pos must not be NULL 197: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30583,23 +31132,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30631,13 +31180,13 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:04:03] +197: [22:06:21] 197: 197: **** 197: Pre-condition Violation @@ -30651,23 +31200,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30699,13 +31248,13 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[02:04:03] +197: .[22:06:21] 197: 197: **** 197: Range Error @@ -30720,23 +31269,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 @@ -30768,13 +31317,13 @@ 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:04:03] +197: [22:06:21] 197: 197: **** 197: Range Error @@ -30788,23 +31337,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30836,13 +31385,13 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[02:04:03] +197: .[22:06:21] 197: 197: **** 197: Range Error @@ -30857,23 +31406,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x00000000005C30D9 in /usr/bin/python3 @@ -30905,13 +31454,13 @@ 197: 51# 0x00000000006820AE in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 54# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:04:03] +197: [22:06:21] 197: 197: **** 197: Pre-condition Violation @@ -30925,23 +31474,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -30973,13 +31522,13 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [02:04:03] +197: [22:06:21] 197: 197: **** 197: Pre-condition Violation @@ -30993,23 +31542,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C9EE5462C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F942FDC162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x00007F9C9C9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x00007F9C9C9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x00007F9C9C9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x00007F9C9C9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x00007F9C9C9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x00007F942D9B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x00007F942D9B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x00007F942D9B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x00007F942D9B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x00007F942D9B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x00007F9C9EE513C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x00007F942FDBE3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x00000000005C30D9 in /usr/bin/python3 @@ -31041,7 +31590,7 @@ 197: 50# 0x00000000006820AE in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x00007F9C9F5FDCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 53# 0x00007F943056ACA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- @@ -31049,724 +31598,250 @@ 197: 197: . 197: ---------------------------------------------------------------------- -197: Ran 9 tests in 0.980s +197: Ran 9 tests in 0.858s 197: 197: OK 197: Testing Trajectory wrapper -195: ........[02:04:03] non-ring atom 0 marked aromatic -195: [02:04:03] non-ring atom 0 marked aromatic -195: [02:04:03] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x00007F8F25484A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x00000000005C30D9 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x000000000064B89F in /usr/bin/python3 -195: 33# 0x000000000069ECA0 in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x00000000005C30D9 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x000000000064B89F in /usr/bin/python3 -195: 39# 0x000000000069ECA0 in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x00000000005C30D9 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x000000000064B89F in /usr/bin/python3 -195: 45# 0x000000000069ECA0 in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x0000000000599C8E in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x000000000066DA21 in /usr/bin/python3 -195: 53# 0x0000000000669A8C in /usr/bin/python3 -195: 54# 0x0000000000682973 in /usr/bin/python3 -195: 55# 0x0000000000682273 in /usr/bin/python3 -195: 56# 0x00000000006820AE in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -195: [02:04:03] non-ring atom 0 marked aromatic -195: [02:04:03] non-ring atom 0 marked aromatic -195: [02:04:03] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 12 < 6 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x00007F8F25484A70 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x00000000005C30D9 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x000000000064B89F in /usr/bin/python3 -195: 33# 0x000000000069ECA0 in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x00000000005C30D9 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x000000000064B89F in /usr/bin/python3 -195: 39# 0x000000000069ECA0 in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x00000000005C30D9 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x000000000064B89F in /usr/bin/python3 -195: 45# 0x000000000069ECA0 in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x0000000000599C8E in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x000000000066DA21 in /usr/bin/python3 -195: 53# 0x0000000000669A8C in /usr/bin/python3 -195: 54# 0x0000000000682973 in /usr/bin/python3 -195: 55# 0x0000000000682273 in /usr/bin/python3 -195: 56# 0x00000000006820AE in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U -160: [02:04:03] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -195: ...............[02:04:03] 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. -195: [02:04:03] 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. -143: [02:04:03] done -143: [02:04:03] ------------------------------------- -143: [02:04:03] Testing GitHubIssue62. -143: [02:04:03] beta-lactam 39.6387 -143: [02:04:03] cyclopropanone 174.698 -143: [02:04:03] aziridine 337.986 -143: [02:04:03] aziridinone 115.248 -160/236 Test #197: pyTestTrajectory ....................... Passed 1.57 sec -test 202 - Start 202: pyCDXMLTest - -202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" -202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -202: Test timeout computed to be: 1500 -143: [02:04:03] isobutene 2.48217 -143: [02:04:03] acetone 1.91788 -143: [02:04:03] cyclopentanone 10.1648 -143: [02:04:03] cyclopropene 99.4921 -143: [02:04:03] cyclobutene 41.0156 -143: [02:04:03] cyclopropane 267.236 -143: [02:04:03] gamma-lactam 15.7471 -143: [02:04:03] trans-2,3-diphenylcyclopropan-1-one 203.398 -195: ..............[02:04:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: [02:04:03] Explicit valence for atom # 1 C, 5, is greater than permitted -148: [02:04:03] Molecule does not have explicit Hs. Consider calling AddHs() -198: ............. -198: ---------------------------------------------------------------------- -198: Ran 13 tests in 0.025s -198: -198: OK -198: Testing SubstanceGroups wrapper -143: [02:04:03] cis-2,3-diphenylcyclopropan-1-one 206.852 -151: 633252489 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -161/236 Test #151: molAlignCatchTest ...................... Passed 4.52 sec -test 203 - Start 203: molStandardizeTest - -203: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -203: Test timeout computed to be: 1500 -201: [02:04:03] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [02:04:03] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [02:04:03] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: .[02:04:03] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [02:04:03] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [02:04:03] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: ...[02:04:03] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [02:04:03] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [02:04:03] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: . -201: ---------------------------------------------------------------------- -201: Ran 5 tests in 0.017s -201: -201: OK -143: [02:04:03] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [02:04:03] cyclopropylidencyclobutane 218.879 -162/236 Test #198: pyTestSGroups .......................... Passed 1.10 sec -test 204 - Start 204: molNormalizeTest - -204: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -204: Test timeout computed to be: 1500 -143: [02:04:04] diphenylmethylidencyclobutane 79.6139 -143: [02:04:04] done -143: [02:04:04] ------------------------------------- -143: [02:04:04] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [02:04:04] done -143: [02:04:04] ------------------------------------- -143: [02:04:04] Test square planar complexes -143: [02:04:04] done -143: [02:04:04] ------------------------------------- -143: [02:04:04] Test octahedral complexes -143: [02:04:04] done -163/236 Test #201: pyTestPropertyLists .................... Passed 0.61 sec -test 205 - Start 205: molValidateTest - -205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -205: Test timeout computed to be: 1500 -164/236 Test #143: testUFFForceFieldHelpers ............... Passed 4.86 sec -test 206 - Start 206: molChargeTest - -206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -206: Test timeout computed to be: 1500 -122: =>start test GETAWAY -122: [02:04:04] test on : 365 molecules done -165/236 Test #122: testGETAWAY ............................ Passed 5.47 sec -test 207 - Start 207: molTautomerTest - -207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -207: Test timeout computed to be: 1500 -204: [02:04:04] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -205: ERROR: [FeaturesValidation] Query atom 0 is not allowed -205: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed -205: ERROR: [FeaturesValidation] Query bond 0 is not allowed -205: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed -205: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed -205: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed -205: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed -205: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed -205: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. -205: here -205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. -205: there -205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -166/236 Test #205: molValidateTest ........................ Passed 0.07 sec -148: [02:04:04] Molecule does not have explicit Hs. Consider calling AddHs() -test 208 - Start 208: molStandardizeSmallTest - -208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -208: Test timeout computed to be: 1500 -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 6.222s -12: -12: OK -167/236 Test #208: molStandardizeSmallTest ................ Passed 0.07 sec -test 209 - Start 209: molFragmentTest - -209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -209: Test timeout computed to be: 1500 -200: .s. -200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.159s -200: -200: OK (skipped=1) -200: Testing Smiles and SD MultithreadedMolSupplier -204: [02:04:04] Initializing Normalizer -204: [02:04:04] Running Normalizer -204: [02:04:04] Rule applied: BrokenazidetoN=N+=N- -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.026s -202: -202: OK -204: [02:04:04] Initializing Normalizer -204: [02:04:04] Running Normalizer -168/236 Test #12: pyBV ................................... Passed 8.62 sec -204: [02:04:04] Initializing Normalizer -204: [02:04:04] Running Normalizer -test 210 - Start 210: molStandardizeCatchTest - -210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -210: Test timeout computed to be: 1500 -169/236 Test #204: molNormalizeTest ....................... Passed 0.22 sec -test 211 - Start 211: molStandardizePipelineTest - -211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -211: Test timeout computed to be: 1500 -170/236 Test #206: molChargeTest .......................... Passed 0.19 sec -test 212 - Start 212: pyMolStandardize - -212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -212: Test timeout computed to be: 1500 -69: [02:04:04] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [02:04:04] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -209: [02:04:04] SMARTS Parse Error: syntax error while parsing: [Cl -209: [02:04:04] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -211: Randomness seeded to: 934354141 -211: 1 Counts line too short: '' on line4 -211: 1 Could not instantiate a valid molecule from input -171/236 Test #209: molFragmentTest ........................ Passed 0.08 sec -test 213 - Start 213: testScaffoldNetwork - -213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -213: Test timeout computed to be: 1500 -211: 8 Molecule has no atoms -211: [02:04:04] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [02:04:04] Explicit valence for atom # 1 N, 4, is greater than permitted -211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -211: 128 An error occurred while preparing the molecule for standardization. -211: 8 The molecule contains an unknown isotope: 3C -148: [02:04:04] Molecule does not have explicit Hs. Consider calling AddHs() -69: [02:04:04] Empty atom list: 'M ALS 1 0 F' on line 8. -211: 4 Query atom 0 is not allowed -172/236 Test #69: fileParsersTest1 ....................... Passed 6.18 sec -test 214 - Start 214: pyScaffoldNetwork - -214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -214: Test timeout computed to be: 1500 -211: 4 Bond 0 of aromatic type is not allowed -211: 4 Bond 1 of aromatic type is not allowed -211: 4 Bond 2 of aromatic type is not allowed -211: 4 Bond 3 of aromatic type is not allowed -211: 4 Bond 5 of aromatic type is not allowed -211: 4 Bond 6 of aromatic type is not allowed -211: 4 Bond 2 of dative type is not allowed -211: 4 Bond 3 of dative type is not allowed -173/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.93 sec -test 215 - Start 215: pyScaffoldNetworkPickling - -215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -215: Test timeout computed to be: 1500 -211: 4 Enhanced stereochemistry features are not allowed -211: 8 The radical at atom 0 is not allowed -211: [02:04:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -174/236 Test #42: resMolSupplierTest ..................... Passed 6.51 sec -test 216 - Start 216: testMolEnumerator - -216: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator -216: Test timeout computed to be: 1500 -211: 16 The molecule includes non-null Z coordinates -175/236 Test #202: pyCDXMLTest ............................ Passed 0.53 sec +177/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 1.10 sec test 217 Start 217: pyMolEnumerator 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 217: Test timeout computed to be: 1500 -211: 32 Atom 0 too close to bond 2 -211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Issue252: Bad definitions for Crippen atom types. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of ChiVs. -211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: [02:04:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of ChiNs. -211: 16 The molecule includes non-null Z coordinates -211: 64 Atom 0 has adjacent stereo bonds with like orientation -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of HallKierAlpha. -211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of Kappa1. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of Kappa2. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of Kappa3. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Crippen atom type calculations. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test ring descriptors -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test other count descriptors. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test MQN -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test GitHub Issue 56. -111: [02:04:04] WARNING: not removing hydrogen atom without neighbors -111: [02:04:04] WARNING: not removing hydrogen atom without neighbors -111: [02:04:04] WARNING: not removing hydrogen atom without neighbors -111: [02:04:04] WARNING: not removing hydrogen atom without neighbors -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github92: Bad Crippen atom type for pyrrole H. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github362: order dependence in Kier-Hall descriptors. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test calculation of spiro and bridgehead counts. -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github694: ExactMolWt ignoring the mass of the electron -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Testing Properties and KitchenSink -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -216: Randomness seeded to: 3698612716 -216: [02:04:04] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -211: 16777216 The representation of some functional groups was adjusted. -111: [02:04:04] ---Caught keyerror (bad property name)--- -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test USR Descriptor -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github #1973: support P and S terms for TPSA calculation -111: [02:04:04] done -111: [02:04:04] ------------------------------------- -111: [02:04:04] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [02:04:04] done -211: 67108864 The protonation state was adjusted. -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. -176/236 Test #111: testDescriptors ........................ Passed 6.08 sec +216: Randomness seeded to: 2883252638 +216: [22:06:21] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +178/236 Test #197: pyTestTrajectory ....................... Passed 1.72 sec test 218 Start 218: testAbbreviations 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 218: Test timeout computed to be: 1500 -211: 16777216 The representation of some functional groups was adjusted. -211: 67108864 The protonation state was adjusted. +210: Randomness seeded to: 1729688210 +210: * - * - * - * m1 +210: * - * - * - * m2 +210: * - * - * - * m1 +210: * - * - * - * m2 216: =============================================================================== 216: All tests passed (321 assertions in 16 test cases) 216: -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -177/236 Test #216: testMolEnumerator ...................... Passed 0.12 sec +179/236 Test #216: testMolEnumerator ...................... Passed 0.22 sec test 219 Start 219: pyAbbreviations 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 219: Test timeout computed to be: 1500 -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -218: Randomness seeded to: 1846553620 -218: [02:04:04] SMARTS Parse Error: syntax error while parsing: *fail -218: [02:04:04] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -211: 8388608 One or more metal atoms were disconnected. -211: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -211: 67108864 The protonation state was adjusted. -218: [02:04:04] no suitable SubstanceGroups found -211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 2 was removed +210: [22:06:21] Can't kekulize mol. Unkekulized atoms: 3 7 +195: ..............[22:06:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: [22:06:21] Explicit valence for atom # 1 C, 5, is greater than permitted +210: [22:06:21] Can't kekulize mol. Unkekulized atoms: 3 8 +218: Randomness seeded to: 1956830236 +218: [22:06:21] SMARTS Parse Error: syntax error while parsing: *fail +218: [22:06:21] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +210: [22:06:21] Can't kekulize mol. Unkekulized atoms: 2 3 4 +150: *********************************************************** +150: Testing O3AAlign +150: --------------------------------- +150: testMMFFO3A +150: +150: --------------------------------- +150: testMMFFO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testMMFFO3A with constraints +150: +150: --------------------------------- +150: testMMFFO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testCrippenO3A +150: +150: --------------------------------- +150: testCrippenO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testCrippenO3A with constraints +150: +150: --------------------------------- +150: testCrippenO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testMMFFO3A multithreading +150: +150: generating reference data +218: [22:06:21] no suitable SubstanceGroups found 218: =============================================================================== 218: All tests passed (195 assertions in 12 test cases) 218: -178/236 Test #218: testAbbreviations ...................... Passed 0.11 sec +180/236 Test #218: testAbbreviations ...................... Passed 0.11 sec test 220 Start 220: generalizedSubstructCatch 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 220: Test timeout computed to be: 1500 -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 1 was removed -148: [02:04:04] Molecule does not have explicit Hs. Consider calling AddHs() -211: 16777216 The "wavy" style of bond 4 was removed -211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -211: 16777216 The "wavy" style of bond 3 was removed -211: 16777216 The representation of some functional groups was adjusted. -211: [02:04:04] Can't kekulize mol. Unkekulized atoms: 2 3 5 -211: =============================================================================== -211: All tests passed (268 assertions in 5 test cases) -211: -179/236 Test #211: molStandardizePipelineTest ............. Passed 0.41 sec +160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +125: Warning: Atom Count for residue GLU5A does not match expected count +125: Warning: Atom Count for residue ASN39A does not match expected count +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +207: [22:06:21] Tautomer enumeration stopped at 292 tautomers: max transforms reached +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test unfolded version of RDKFP +128: [22:06:21] ------------------------------------- +128: [22:06:21] Test bitinfo of RDKFP +128: 562: [ 2 ], +128: 709: [ 0 1 ], +128: 1118: [ 0 1 2 ], +128: 1183: [ 1 2 ], +128: 1233: [ 0 1 2 ], +128: 1308: [ 0 ], [ 1 ], +128: 1339: [ 2 ], +128: 1728: [ 1 2 ], +128: 1772: [ 0 ], [ 1 ], +128: 1813: [ 0 1 ], +128: ------------ +128: [22:06:21] ------------------------------------- +128: [22:06:21] Single atoms setting radius 1 bits in Morgan fingerprints +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use AtomPairGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #2115: BitInfo not complete for RDKFingerprint +128: [22:06:21] done +128: [22:06:21] ------------------------------------- +128: [22:06:21] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [22:06:21] done +181/236 Test #128: testFingerprints ....................... Passed 10.31 sec +214: ....... +214: ---------------------------------------------------------------------- +214: Ran 7 tests in 0.048s +214: +214: OK test 221 Start 221: pyGeneralizedSubstruct 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 221: Test timeout computed to be: 1500 -195: ............................[02:04:04] unable to set wavy bonds for double bonds: 3 -210: Randomness seeded to: 3844587694 -210: * - * - * - * m1 -210: * - * - * - * m2 -210: * - * - * - * m1 -210: * - * - * - * m2 -210: [02:04:04] Can't kekulize mol. Unkekulized atoms: 3 7 -210: [02:04:04] Can't kekulize mol. Unkekulized atoms: 3 8 -210: [02:04:04] Can't kekulize mol. Unkekulized atoms: 2 3 4 -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 6.773s -169: -169: OK -195: .............[02:04:07] -195: -195: **** -195: Range Error -195: idx -195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -195: Failed Expression: 6 < 5 -195: ---------- -195: Stacktrace: -195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 28# _PyObject_MakeTpCall in /usr/bin/python3 -195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 30# 0x00000000005C30D9 in /usr/bin/python3 -195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 32# 0x000000000064B89F in /usr/bin/python3 -195: 33# 0x000000000069ECA0 in /usr/bin/python3 -195: 34# _PyObject_MakeTpCall in /usr/bin/python3 -195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 36# 0x00000000005C30D9 in /usr/bin/python3 -195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 38# 0x000000000064B89F in /usr/bin/python3 -195: 39# 0x000000000069ECA0 in /usr/bin/python3 -195: 40# _PyObject_MakeTpCall in /usr/bin/python3 -195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 42# 0x00000000005C30D9 in /usr/bin/python3 -195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 44# 0x000000000064B89F in /usr/bin/python3 -195: 45# 0x000000000069ECA0 in /usr/bin/python3 -195: 46# _PyObject_MakeTpCall in /usr/bin/python3 -195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 48# 0x0000000000599C8E in /usr/bin/python3 -195: 49# _PyObject_MakeTpCall in /usr/bin/python3 -195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -195: 51# PyEval_EvalCode in /usr/bin/python3 -195: 52# 0x000000000066DA21 in /usr/bin/python3 -195: 53# 0x0000000000669A8C in /usr/bin/python3 -195: 54# 0x0000000000682973 in /usr/bin/python3 -195: 55# 0x0000000000682273 in /usr/bin/python3 -195: 56# 0x00000000006820AE in /usr/bin/python3 -195: 57# Py_RunMain in /usr/bin/python3 -195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 -195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -195: 61# _start in /usr/bin/python3 -195: ---------- -195: **** -195: -160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U -217: ... -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.029s -217: -217: OK -180/236 Test #169: pyMMPA ................................. Passed 7.22 sec -160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U +160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U +182/236 Test #214: pyScaffoldNetwork ...................... Passed 0.56 sec test 222 Start 222: testMolProcessing 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing 222: Test timeout computed to be: 1500 -148: [02:04:07] Molecule does not have explicit Hs. Consider calling AddHs() -207: [02:04:07] Tautomer enumeration stopped at 292 tautomers: max transforms reached -181/236 Test #217: pyMolEnumerator ........................ Passed 3.10 sec +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U +183/236 Test #125: descriptorsTestCatch ................... Passed 10.47 sec test 223 Start 223: pyMolProcessing 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 223: Test timeout computed to be: 1500 -160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U -214: ....... -214: ---------------------------------------------------------------------- -214: Ran 7 tests in 0.159s -214: -214: OK -148: [02:04:07] Molecule does not have explicit Hs. Consider calling AddHs() -163: [02:04:07] The provided InitialSeed is not an MCS and will be ignored -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() 215: . 215: ---------------------------------------------------------------------- -215: Ran 1 test in 0.047s +215: Ran 1 test in 0.015s 215: 215: OK -182/236 Test #214: pyScaffoldNetwork ...................... Passed 3.40 sec +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 0.031s +217: +217: OK +184/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.67 sec test 224 Start 224: testMIF 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields 224: Test timeout computed to be: 1500 -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 5.738s -189: -189: OK -146: validating reference data -160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U -220: Randomness seeded to: 961007230 -220: =============================================================================== -220: All tests passed (486 assertions in 10 test cases) -220: -183/236 Test #220: generalizedSubstructCatch .............. Passed 3.28 sec +160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +185/236 Test #217: pyMolEnumerator ........................ Passed 0.60 sec test 225 Start 225: pyMIF 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 225: Test timeout computed to be: 1500 -184/236 Test #189: pyRGroupDecomposition .................. Passed 6.22 sec +160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U +160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U +160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U +160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +220: Randomness seeded to: 3728083144 +220: =============================================================================== +220: All tests passed (486 assertions in 10 test cases) +220: +186/236 Test #220: generalizedSubstructCatch .............. Passed 0.39 sec test 226 Start 226: testQuery @@ -31790,13 +31865,18 @@ 226: XOr 226: pointer and copy foo 226: Set2 -185/236 Test #226: testQuery .............................. Passed 0.01 sec +187/236 Test #226: testQuery .............................. Passed 0.02 sec test 227 Start 227: testBaseFeatures 227: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures 227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features 227: Test timeout computed to be: 1500 +163: [22:06:22] The provided InitialSeed is not an MCS and will be ignored +224: Randomness seeded to: 4238237367 +224: =============================================================================== +224: All tests passed (27926 assertions in 8 test cases) +224: 227: ------------------------------------- 227: Basics for ExplicitFeatures. 227: done @@ -31806,13 +31886,33 @@ 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done -186/236 Test #227: testBaseFeatures ....................... Passed 0.01 sec +188/236 Test #224: testMIF ................................ Passed 0.14 sec +189/236 Test #227: testBaseFeatures ....................... Passed 0.02 sec test 228 Start 228: testMatCalc 228: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 228: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc 228: Test timeout computed to be: 1500 +test 229 + Start 229: pyMatCalc + +229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +229: Test timeout computed to be: 1500 +160: [22:06:22] 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. +219: ....... +219: ---------------------------------------------------------------------- +219: Ran 7 tests in 0.037s +219: +219: OK +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 2.998s +189: +189: OK +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +212: .....[22:06:22] Tautomer enumeration stopped at 292 tautomers: max transforms reached 228: 1.68022e+08 228: 1.73149e+08 228: 1.05549e+08 @@ -31858,239 +31958,164 @@ 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 -187/236 Test #228: testMatCalc ............................ Passed 0.01 sec -test 229 - Start 229: pyMatCalc - -229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -229: Test timeout computed to be: 1500 -224: Randomness seeded to: 3974183698 -224: =============================================================================== -224: All tests passed (27926 assertions in 8 test cases) -224: -188/236 Test #224: testMIF ................................ Passed 0.16 sec +190/236 Test #189: pyRGroupDecomposition .................. Passed 6.36 sec +191/236 Test #219: pyAbbreviations ........................ Passed 0.73 sec +192/236 Test #228: testMatCalc ............................ Passed 0.15 sec test 230 Start 230: testSimDivPickers 230: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 -230: [02:04:07] ------------------------------------- -230: [02:04:07] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [02:04:07] Done -230: [02:04:07] ------------------------------------- -230: [02:04:07] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [02:04:07] Done -189/236 Test #230: testSimDivPickers ...................... Passed 0.02 sec test 231 Start 231: pickersTestsCatch 231: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 231: Test timeout computed to be: 1500 -190/236 Test #215: pyScaffoldNetworkPickling .............. Passed 3.58 sec test 232 Start 232: pySimDivPickers 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 232: Test timeout computed to be: 1500 -160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.385s -221: -221: OK -212: .....[02:04:08] Tautomer enumeration stopped at 292 tautomers: max transforms reached -160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U -160: file github5383_2.svg gave hash 2560846108U not the expected 0U -219: ....... -219: ---------------------------------------------------------------------- -219: Ran 7 tests in 0.064s -219: -219: OK -191/236 Test #221: pyGeneralizedSubstruct ................. Passed 3.44 sec +195: ............................[22:06:22] unable to set wavy bonds for double bonds: 3 +160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U +207: [22:06:22] Tautomer enumeration stopped at 292 tautomers: max transforms reached +212: [22:06:22] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +230: [22:06:22] ------------------------------------- +230: [22:06:22] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [22:06:22] Done +230: [22:06:22] ------------------------------------- +230: [22:06:22] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [22:06:22] Done +193/236 Test #230: testSimDivPickers ...................... Passed 0.05 sec test 233 Start 233: pyRanker 233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 233: Test timeout computed to be: 1500 -160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U -231: Randomness seeded to: 2025877293 +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +207: [22:06:22] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +195: .............[22:06:22] +195: +195: **** +195: Range Error +195: idx +195: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +195: Failed Expression: 6 < 5 +195: ---------- +195: Stacktrace: +195: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 28# _PyObject_MakeTpCall in /usr/bin/python3 +195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 30# 0x00000000005C30D9 in /usr/bin/python3 +195: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 32# 0x000000000064B89F in /usr/bin/python3 +195: 33# 0x000000000069ECA0 in /usr/bin/python3 +195: 34# _PyObject_MakeTpCall in /usr/bin/python3 +195: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 36# 0x00000000005C30D9 in /usr/bin/python3 +195: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 38# 0x000000000064B89F in /usr/bin/python3 +195: 39# 0x000000000069ECA0 in /usr/bin/python3 +195: 40# _PyObject_MakeTpCall in /usr/bin/python3 +195: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 42# 0x00000000005C30D9 in /usr/bin/python3 +195: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 44# 0x000000000064B89F in /usr/bin/python3 +195: 45# 0x000000000069ECA0 in /usr/bin/python3 +195: 46# _PyObject_MakeTpCall in /usr/bin/python3 +195: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 48# 0x0000000000599C8E in /usr/bin/python3 +195: 49# _PyObject_MakeTpCall in /usr/bin/python3 +195: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +195: 51# PyEval_EvalCode in /usr/bin/python3 +195: 52# 0x000000000066DA21 in /usr/bin/python3 +195: 53# 0x0000000000669A8C in /usr/bin/python3 +195: 54# 0x0000000000682973 in /usr/bin/python3 +195: 55# 0x0000000000682273 in /usr/bin/python3 +195: 56# 0x00000000006820AE in /usr/bin/python3 +195: 57# Py_RunMain in /usr/bin/python3 +195: 58# Py_BytesMain in /usr/bin/python3 +195: 59# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +195: 61# _start in /usr/bin/python3 +195: ---------- +195: **** +195: +231: Randomness seeded to: 609549674 231: =============================================================================== 231: All tests passed (21267 assertions in 1 test case) 231: -192/236 Test #231: pickersTestsCatch ...................... Passed 0.21 sec +194/236 Test #231: pickersTestsCatch ...................... Passed 0.12 sec test 234 Start 234: testChemicalFeatures 234: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures 234: Test timeout computed to be: 1500 -160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U 234: ----------------------------------------- 234: Test1 234: Done -193/236 Test #234: testChemicalFeatures ................... Passed 0.01 sec +195/236 Test #234: testChemicalFeatures ................... Passed 0.01 sec test 235 Start 235: pyFeatures 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 235: Test timeout computed to be: 1500 -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -223: .. -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.260s -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -223: -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -223: OK -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test unfolded version of RDKFP -128: [02:04:08] ------------------------------------- -128: [02:04:08] Test bitinfo of RDKFP -128: 562: [ 2 ], -128: 709: [ 0 1 ], -128: 1118: [ 0 1 2 ], -128: 1183: [ 1 2 ], -128: 1233: [ 0 1 2 ], -128: 1308: [ 0 ], [ 1 ], -128: 1339: [ 2 ], -128: 1728: [ 1 2 ], -128: 1772: [ 0 ], [ 1 ], -128: 1813: [ 0 1 ], -128: ------------ -128: [02:04:08] ------------------------------------- -128: [02:04:08] Single atoms setting radius 1 bits in Morgan fingerprints -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #2115: BitInfo not complete for RDKFingerprint -128: [02:04:08] done -128: [02:04:08] ------------------------------------- -128: [02:04:08] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [02:04:08] done -194/236 Test #128: testFingerprints ....................... Passed 9.46 sec +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() +196/236 Test #203: molStandardizeTest ..................... Passed 2.12 sec test 236 Start 236: pythonProjectTests 236: Test command: /usr/bin/python3 "-m" "pytest" 236: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects 236: Test timeout computed to be: 1500 -207: [02:04:08] Tautomer enumeration stopped at 292 tautomers: max transforms reached -212: [02:04:08] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -160: [02:04:08] 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. -195/236 Test #219: pyAbbreviations ........................ Passed 3.80 sec +160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 186: iterative -160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U -196/236 Test #223: pyMolProcessing ........................ Passed 0.86 sec -207: [02:04:08] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +207: [22:06:22] Tautomer enumeration stopped at 23 tautomers: canceled +207: Enumeration was canceled due to timeout (50 ms) +148: [22:06:22] Molecule does not have explicit Hs. Consider calling AddHs() 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -171: Randomness seeded to: 4258197510 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -232: [02:04:08] the useCache argument is deprecated and ignored -212: .[02:04:08] Tautomer enumeration stopped at 43 tautomers: canceled -212: Enumeration was canceled due to timeout (50 ms) -150: *********************************************************** -150: Testing O3AAlign -150: --------------------------------- -150: testMMFFO3A -150: -150: --------------------------------- -150: testMMFFO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testMMFFO3A with constraints -150: -150: --------------------------------- -150: testMMFFO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testCrippenO3A -150: -150: --------------------------------- -150: testCrippenO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testCrippenO3A with constraints -150: -150: --------------------------------- -150: testCrippenO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testMMFFO3A multithreading -150: -150: generating reference data -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 7 tests in 0.224s -225: -225: OK -225: Testing MIF wrapper -160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -29: All 191 tests passed -148: .[02:04:08] Molecule does not have explicit Hs. Consider calling AddHs() -197/236 Test #225: pyMIF .................................. Passed 0.87 sec -233: ..[02:04:08] +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +233: ..[22:06:22] 233: 233: **** +232: [22:06:22] the useCache argument is deprecated and ignored 233: Invariant Violation 233: Can't rank more bits than the ensemble size 233: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp @@ -32103,14 +32128,14 @@ 233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -233: 6# 0x00007F0CD6DDF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x00007F8A0E8DF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -233: 13# 0x00007F0CD6DDC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x00007F8A0E8DC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 233: 14# _PyObject_MakeTpCall in /usr/bin/python3 233: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 233: 16# 0x00000000005C30D9 in /usr/bin/python3 @@ -32142,7 +32167,7 @@ 233: 42# 0x00000000006820AE in /usr/bin/python3 233: 43# Py_RunMain in /usr/bin/python3 233: 44# Py_BytesMain in /usr/bin/python3 -233: 45# 0x00007F0CD858ECA8 in /lib/x86_64-linux-gnu/libc.so.6 +233: 45# 0x00007F8A0FAFFCA8 in /lib/x86_64-linux-gnu/libc.so.6 233: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 233: 47# _start in /usr/bin/python3 233: ---------- @@ -32150,1268 +32175,134 @@ 233: 233: ... 233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.057s +233: Ran 5 tests in 0.041s 233: 233: OK -198/236 Test #203: molStandardizeTest ..................... Passed 4.77 sec +171: Randomness seeded to: 20772834 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.304s +221: +221: OK +197/236 Test #233: pyRanker ............................... Passed 0.56 sec +198/236 Test #221: pyGeneralizedSubstruct ................. Passed 1.11 sec +212: .[22:06:23] Tautomer enumeration stopped at 15 tautomers: canceled +212: Enumeration was canceled due to timeout (50 ms) +232: ...[22:06:23] the useCache argument is deprecated and ignored +232: [22:06:23] the useCache argument is deprecated and ignored +232: .[22:06:23] the useCache argument is deprecated and ignored +213: Randomness seeded to: 1279858062 +213: =============================================================================== +213: All tests passed (273 assertions in 19 test cases) +213: 235: .. 235: ---------------------------------------------------------------------- 235: Ran 2 tests in 0.001s 235: 235: OK 235: Testing ChemicalFeatures Wrapper code: -232: ...[02:04:08] the useCache argument is deprecated and ignored -232: [02:04:08] the useCache argument is deprecated and ignored -199/236 Test #233: pyRanker ............................... Passed 0.73 sec -232: .[02:04:08] the useCache argument is deprecated and ignored -117: =>start test GETAWAY custom -117: [02:04:08] test on : 365 molecules done -200/236 Test #117: testRDFcustom .......................... Passed 10.45 sec -201/236 Test #235: pyFeatures ............................. Passed 0.77 sec -207: [02:04:08] Tautomer enumeration stopped at 33 tautomers: canceled -207: Enumeration was canceled due to timeout (50 ms) -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +199/236 Test #213: testScaffoldNetwork .................... Passed 1.99 sec +200/236 Test #235: pyFeatures ............................. Passed 0.54 sec +29: All 191 tests passed 229: ..... 229: ---------------------------------------------------------------------- -229: Ran 5 tests in 0.856s +229: Ran 5 tests in 0.385s 229: 229: OK -202/236 Test #229: pyMatCalc .............................. Passed 1.39 sec -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -203/236 Test #125: descriptorsTestCatch ................... Passed 10.86 sec -160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U -173: [02:04:09] Building the fingerprints may take some time. -213: Randomness seeded to: 3884509965 -213: =============================================================================== -213: All tests passed (273 assertions in 19 test cases) -213: -204/236 Test #213: testScaffoldNetwork .................... Passed 5.54 sec -160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U -164: ........................................[02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: .[02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: .[02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -195: ....................[02:04:10] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:10] Explicit valence for atom # 6 F, 2, is greater than permitted -195: [02:04:10] Can't kekulize mol. Unkekulized atoms: 3 4 5 -160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U -164: .[02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -164: [02:04:10] The provided InitialSeed is not an MCS and will be ignored -160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U -232: ....... -232: ---------------------------------------------------------------------- -232: Ran 11 tests in 2.330s -232: -232: OK +223: .. +223: ---------------------------------------------------------------------- +223: Ran 2 tests in 0.770s +223: +223: OK +201/236 Test #223: pyMolProcessing ........................ Passed 1.41 sec +202/236 Test #229: pyMatCalc .............................. Passed 1.04 sec +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 7 tests in 0.548s +225: +225: OK +225: Testing MIF wrapper +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +148: .[22:06:23] Molecule does not have explicit Hs. Consider calling AddHs() 186: bulk -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 10.286s -164: -164: OK -205/236 Test #232: pySimDivPickers ........................ Passed 2.83 sec -206/236 Test #164: pyFMCS ................................. Passed 10.80 sec -195: .................[02:04:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +117: =>start test GETAWAY custom +203/236 Test #225: pyMIF .................................. Passed 1.58 sec +117: [22:06:23] test on : 365 molecules done 207: 375 207: Enumeration has completed -160: =============================================================================== -160: All tests passed (6857 assertions in 116 test cases) -160: -207/236 Test #160: moldraw2DTestCatch ..................... Passed 11.46 sec -173: [02:04:11] -173: -173: **** -173: Invariant Violation -173: molzip: bond info not properly setup for bgn atom with label:1 -173: Violation occurred on line 1090 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -173: Failed Expression: bond.a -173: ---------- -173: Stacktrace: -173: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -173: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -173: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 7# 0x000056299BC7956A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x000056299BCC3D78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x000056299BCC4898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x000056299BCC4D10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x000056299BC962C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x000056299BC9662C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x000056299BC7878E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x00007FEBFCE33CA8 in /lib/x86_64-linux-gnu/libc.so.6 -173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -173: 16# 0x000056299BC787D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: ---------- -173: **** -173: -173: [02:04:11] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) -173: molzip: bond info not properly setup for bgn atom with label:1 -173: [02:04:11] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [02:04:11] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) -173: Explicit valence for atom # 4 C, 5, is greater than permitted -173: [02:04:11] Complex queries can be slow. -212: Enumeration has completed -207: [02:04:11] Tautomer enumeration stopped at 22 tautomers: canceled -212: [02:04:11] Tautomer enumeration stopped at 25 tautomers: canceled -170: Randomness seeded to: 3523958850 -170: [02:04:11] Timed out after 11 seconds. -173: [02:04:11] Complex queries can be slow. -236: ============================= test session starts ============================== -236: platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 -236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects -236: configfile: pytest.ini -236: collected 12 items -236: -173: [02:04:11] Complex queries can be slow. -212: ..........[02:04:11] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [02:04:11] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [02:04:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [02:04:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -173: [02:04:12] Complex queries can be slow. -74: [02:04:12] Finished: testSmiCorrectness() -74: [02:04:12] ----------------------------------------- +207: [22:06:23] Tautomer enumeration stopped at 74 tautomers: canceled +74: [22:06:23] Finished: testSmiCorrectness() +74: [22:06:23] ----------------------------------------- 74: -74: [02:04:12] +74: [22:06:23] 74: ----------------------------------------- -74: [02:04:12] Spurious data before the first property will be ignored -74: [02:04:12] Property will be truncated after the first blank line -74: [02:04:12] Property will be truncated after the first blank line -74: [02:04:12] Property will be truncated after the first blank line -222: Randomness seeded to: 136513302 -222: =============================================================================== -222: All tests passed (203 assertions in 1 test case) -222: -208/236 Test #222: testMolProcessing ...................... Passed 5.05 sec -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -173: [02:04:12] Complex queries can be slow. -173: [02:04:12] Complex queries can be slow. -183: [02:04:12] ------------------------------------- -183: [02:04:12] testing PatternHolder -74: [02:04:12] Finished: testSDCorrectness() -74: [02:04:12] ----------------------------------------- -74: -209/236 Test #74: testMultithreadedMolSupplier ........... Passed 14.71 sec -186: bulk, no symmetry -173: [02:04:13] Complex queries can be slow. -183: [02:04:13] ------------------------------------- -183: [02:04:13] testing TautomerPatternHolder -173: [02:04:13] Complex queries can be slow. -207: CN=c1cc[nH]cn1 -207: CN=c1ccnc[nH]1 -207: CNc1ccncn1 -207: res: CNc1ccncn1 -207: CN=c1cccc[nH]1 -207: CNc1ccccn1 -207: res: CNc1ccccn1 -183: [02:04:13] ------------------------------------- -183: [02:04:13] testSegFaultInHolder -183: [02:04:13] SMILES Parse Error: syntax error while parsing: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: dsafsdf[02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: -183: [02:04:13] SMILES[02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES[02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error[02:04:13] [02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position Parse Error: Failed parsing SMILES 'dsafsdf'[02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: [02:04:13] SMILES Parse Error: syntax error[02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: syntax error while parsing: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position dsafsdf[02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position dsafsdfSMILES Parse Error: 1Failed parsing SMILES 'dsafsdf'1 for input: ': -183: [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: : -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] -183: ^ -183: [02:04:13] dsafsdf -183: syntax error[02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf while parsing: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: ':[02:04:13] ^ -183: [02:04:13] dsafsdf -183: -183: -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[02:04:13] dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position -183: [02:04:13] SMILES1: -183: Parse Error: [02:04:13] [02:04:13] ^ -183: dsafsdf[02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[02:04:13] -183: [02:04:13] for input: 'dsafsdf' -183: ^ -183: SMILES Parse Error: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1[02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ for input: 'dsafsdf' -183: [02:04:13] [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf[02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] [02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] [02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: [02:04:13] [02:04:13] [02:04:13] [02:04:13] -183: SMILES Parse Error: syntax error while parsing: [02:04:13] dsafsdf -183: syntax error[02:04:13] [02:04:13] SMILES Parse Error: SMILES Parse Error: check for mistakes around position [02:04:13] [02:04:13] SMILES Parse Error: SMILES Parse Error: syntax errorsyntax errorSMILES Parse Error: syntax error[02:04:13] [02:04:13] SMILES Parse Error: while parsing: [02:04:13] SMILES Parse Error: 1SMILES Parse Error: [02:04:13] : -183: [02:04:13] dsafsdf -183: [02:04:13] ^ while parsing: dsafsdfsyntax error while parsing: dsafsdfSMILES Parse Error: check for mistakes around position [02:04:13] SMILES Parse Error: syntax errorSMILES Parse Error: 1SMILES Parse Error: [02:04:13] syntax error while parsing: dsafsdfSMILES Parse Error: syntax error: while parsing: dsafsdf -183: SMILESdsafsdfsyntax error -183: [02:04:13] SMILES Parse Error: check for mistakes around position 11: -183: [02:04:13] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error: while parsing: SMILES Parse Error: check for mistakes around position -183: -183: syntax errordsafsdf while parsing: syntax error -183: while parsing: while parsing: syntax errordsafsdfsyntax error while parsing: -183: SMILES Parse Error: -183: syntax error -183: -183: Parse Error: [02:04:13] while parsing: dsafsdfdsafsdf -183: SMILES Parse Error: check for mistakes around position 1:dsafsdfSMILES Parse Error: -183: syntax error[02:04:13] SMILES Parse Error: check for mistakes around position -183: 1::dsafsdf1[02:04:13] :SMILES Parse Error: -183: syntax error[02:04:13] while parsing: -183: -183: while parsing: while parsing: dsafsdfdsafsdf -183: -183: dsafsdf -183: Failed parsing SMILES 'dsafsdf' -183: for input: ' -183: [02:04:13] dsafsdf[02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position 1 while parsing: :SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: -183: dsafsdf while parsing: [02:04:13] SMILES Parse Error: dsafsdf'[02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] dsafsdf -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' -183: SMILES Parse Error: check for mistakes around position -183: [02:04:13] [02:04:13] dsafsdf -183: [02:04:13] while parsing: SMILES Parse Error: check for mistakes around position 1[02:04:13] dsafsdf -183: SMILES Parse Error: check for mistakes around position [02:04:13] SMILES -183: SMILES Parse Error: check for mistakes around position Parse Error: dsafsdfdsafsdf[02:04:13] [02:04:13] 1 for input: ': -183: -183: 1[02:04:13] [02:04:13] [02:04:13] ^: -183: -183: dsafsdf -183: :dsafsdf -183: dsafsdfSMILES Parse Error: check for mistakes around position [02:04:13] -183: 1^: -183: [02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] -183: dsafsdfSMILES Parse Error: check for mistakes around position -183: 1: -183: -183: ^[02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position dsafsdf[02:04:13] [02:04:13] ^[02:04:13] -183: dsafsdf^ -183: -183: -183: [02:04:13] [02:04:13] [02:04:13] '[02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position SMILES Parse Error: [02:04:13] -183: ^ -183: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[02:04:13] -183: 11::SMILES Parse Error: check for mistakes around position -183: 1: -183: [02:04:13] [02:04:13] Failed parsing SMILES 'dsafsdf' for input: '[02:04:13] SMILESSMILES Parse Error: check for mistakes around position for input: 'dsafsdf[02:04:13] 'dsafsdfSMILES -183: [02:04:13] ^ -183: Parse Error: Failed parsing SMILES 'dsafsdf'SMILES -183: SMILES Parse Error: -183: syntax errorSMILES Parse Error: -183: Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf -183: 1 for input: ': -183: [02:04:13] SMILES Parse Error: check for mistakes around position [02:04:13] while parsing: -183: [02:04:13] [02:04:13] -183: Parse Error: dsafsdf[02:04:13] SMILES^dsafsdf[02:04:13] 11dsafsdf^:dsafsdfSMILES: Parse Error: -183: [02:04:13] [02:04:13] -183: Failed parsing SMILES 'dsafsdf' -183: for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf^dsafsdf[02:04:13] 'dsafsdf[02:04:13] '^ -183: ' -183: -183: [02:04:13] ^ -183: -183: ^'[02:04:13] -183: dsafsdf Parse Error: -183: [02:04:13] [02:04:13] [02:04:13] ^ -183: Failed parsing SMILES 'dsafsdf' for input: ' -183: [02:04:13] dsafsdf'[02:04:13] SMILES -183: -183: Parse Error: [02:04:13] [02:04:13] for input: ' -183: -183: 'dsafsdf -183: -183: [02:04:13] ^ Parse Error: ^dsafsdf -183: dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1[02:04:13] -183: SMILES[02:04:13] ^Failed parsing SMILES 'dsafsdf'[02:04:13] for input: '[02:04:13] [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' Parse Error: dsafsdf' -183: -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: check for mistakes around position -183: -183: [02:04:13] SMILES[02:04:13] SMILES^ -183: Parse Error: 1^[02:04:13] :Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: SMILESdsafsdfFailed parsing SMILES 'dsafsdf' for input: ' -183: Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: [02:04:13] [02:04:13] SMILES Parse Error: dsafsdfSMILESdsafsdfFailed parsing SMILES 'dsafsdf'' -183: [02:04:13] 'SMILES Parse Error: -183: -183: -183: Failed parsing SMILES 'dsafsdf'[02:04:13] for input: ' -183: :dsafsdf -183: SMILES[02:04:13] Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[02:04:13] SMILES Parse Error: dsafsdf[02:04:13] dsafsdf -183: Failed parsing SMILES 'dsafsdf'' Parse Error: for input: 'dsafsdf -183: ' -183: [02:04:13] '^ -183: -183: for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] ^ -183: [02:04:13] [02:04:13] ^SMILES Parse Error: [02:04:13] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'dsafsdf -183: [02:04:13] Failed parsing SMILES 'dsafsdf' -183: -183: for input: 'Failed parsing SMILES 'dsafsdf' for input: ''SMILES -183: Parse Error: [02:04:13] SMILESdsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: dsafsdf Parse Error: -183: dsafsdf[02:04:13] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: ' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: for input: 'dsafsdf' -183: ' -183: [02:04:13] ^[02:04:13] SMILES Parse Error: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] [02:04:13] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error while parsing: dsafsdf -183: [02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position 1 -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: -183: syntax error[02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax errordsafsdf while parsing: while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: 1: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1[02:04:13] SMILES[02:04:13] 1: -183: [02:04:13] :[02:04:13] -183: -183: dsafsdf -183: [02:04:13] dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] Parse Error: dsafsdf -183: [02:04:13] Failed parsing SMILES 'dsafsdf'[02:04:13] [02:04:13] [02:04:13] SMILES Parse Error: ^ -183: -183: SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] [02:04:13] ^ -183: [02:04:13] SMILES^SMILES Parse Error: check for mistakes around position Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: for input: 'dsafsdf' -183: SMILES Parse Error: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [02:04:13] SMILES Parse Error: check for mistakes around position 1: -183: [02:04:13] dsafsdf -183: [02:04:13] ^ -183: [02:04:13] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [02:04:13] ------------------------------------- -183: [02:04:13] Results do not depend on numThreads -173: [02:04:13] Complex queries can be slow. -212: ............[02:04:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [02:04:13] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: [02:04:13] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -210/236 Test #207: molTautomerTest ........................ Passed 9.69 sec -173: [02:04:13] Complex queries can be slow. -186: [02:04:14] Relabelling existing label -212: ........[02:04:16] Explicit valence for atom # 1 O, 3, is greater than permitted -186: Best mapping -212: .. -212: ---------------------------------------------------------------------- -212: Ran 38 tests in 9.268s -212: -212: OK -212: done -211/236 Test #212: pyMolStandardize ....................... Passed 12.46 sec +74: [22:06:24] Spurious data before the first property will be ignored +74: [22:06:24] Property will be truncated after the first blank line +74: [22:06:24] Property will be truncated after the first blank line +74: [22:06:24] Property will be truncated after the first blank line +146: validating reference data +204/236 Test #117: testRDFcustom .......................... Passed 12.87 sec 126: Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count -212/236 Test #199: pyTestThreads .......................... Passed 13.81 sec 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -126: .[02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: .[02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: ..[02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: [02:04:16] DEPRECATION WARNING: please use MorganGenerator -126: ....[02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:04:16] DEPRECATION WARNING: please use AtomPairGenerator -126: .[02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:04:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: .[22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: ..[22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: .[22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: [22:06:24] DEPRECATION WARNING: please use MorganGenerator +126: ....[22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: [22:06:24] DEPRECATION WARNING: please use AtomPairGenerator +126: .[22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [22:06:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 17.481s +126: Ran 31 tests in 11.833s 126: 126: OK 126: exactmw 78.046950192 @@ -33460,9 +32351,133 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -173: [02:04:16] Complex queries can be slow. -213/236 Test #186: testRGroupDecomp ....................... Passed 15.49 sec -214/236 Test #126: pyMolDescriptors ....................... Passed 18.22 sec +205/236 Test #126: pyMolDescriptors ....................... Passed 12.73 sec +164: ........................................[22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: .[22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: .[22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: .[22:06:24] The provided InitialSeed is not an MCS and will be ignored +173: [22:06:24] Building the fingerprints may take some time. +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: [22:06:24] The provided InitialSeed is not an MCS and will be ignored +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 10.422s +164: +164: OK +74: [22:06:24] Finished: testSDCorrectness() +74: [22:06:24] ----------------------------------------- +74: +206/236 Test #74: testMultithreadedMolSupplier ........... Passed 14.08 sec +170: Randomness seeded to: 2287988609 +170: [22:06:26] Timed out after 12 seconds. +186: bulk, no symmetry +207/236 Test #164: pyFMCS ................................. Passed 13.51 sec +207: CN=c1cc[nH]cn1 +207: CN=c1ccnc[nH]1 +207: CNc1ccncn1 +207: res: CNc1ccncn1 +207: CN=c1cccc[nH]1 +207: CNc1ccccn1 +207: res: CNc1ccccn1 +160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U +232: ....... +232: ---------------------------------------------------------------------- +232: Ran 11 tests in 4.336s +232: +232: OK +208/236 Test #232: pySimDivPickers ........................ Passed 4.82 sec +209/236 Test #207: molTautomerTest ........................ Passed 6.32 sec +186: [22:06:27] Relabelling existing label +173: [22:06:27] +173: +173: **** +173: Invariant Violation +173: molzip: bond info not properly setup for bgn atom with label:1 +173: Violation occurred on line 1090 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +173: Failed Expression: bond.a +173: ---------- +173: Stacktrace: +173: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +173: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +173: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 +173: 7# 0x000055983074D56A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000559830797D78 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000559830798898 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000559830798D10 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x000055983076A2C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x000055983076A62C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x000055983074C78E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x00007FC2AD833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +173: 16# 0x000055983074C7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: ---------- +173: **** +173: +173: [22:06:27] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: molzip: bond info not properly setup for bgn atom with label:1 +173: [22:06:27] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [22:06:27] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: Explicit valence for atom # 4 C, 5, is greater than permitted +173: [22:06:27] Complex queries can be slow. +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +195: ....................[22:06:27] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:27] Explicit valence for atom # 6 F, 2, is greater than permitted +195: [22:06:27] Can't kekulize mol. Unkekulized atoms: 3 4 5 +186: Best mapping +160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U +160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U +173: [22:06:27] Complex queries can be slow. +210/236 Test #186: testRGroupDecomp ....................... Passed 12.28 sec +195: .................[22:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U +173: [22:06:28] Complex queries can be slow. +212: Enumeration has completed +212: [22:06:28] Tautomer enumeration stopped at 47 tautomers: canceled +173: [22:06:28] Complex queries can be slow. +160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +212: ..........[22:06:28] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [22:06:28] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [22:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [22:06:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +173: [22:06:28] Complex queries can be slow. +222: Randomness seeded to: 974458954 +222: =============================================================================== +222: All tests passed (203 assertions in 1 test case) +222: +211/236 Test #222: testMolProcessing ...................... Passed 6.67 sec +173: [22:06:28] Complex queries can be slow. +160: =============================================================================== +160: All tests passed (6857 assertions in 116 test cases) +160: +212/236 Test #160: moldraw2DTestCatch ..................... Passed 15.89 sec +173: [22:06:29] Complex queries can be slow. +173: [22:06:29] Complex queries can be slow. +173: [22:06:29] Complex queries can be slow. +173: [22:06:29] Complex queries can be slow. +173: [22:06:30] Complex queries can be slow. +236: ============================= test session starts ============================== +236: platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 +236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects +236: configfile: pytest.ini +236: collected 12 items +236: +212: ............[22:06:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [22:06:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: [22:06:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done @@ -33474,9 +32489,18 @@ 159: file test3_5.png gave hash 3317652686U not the expected 3842605920U 159: file test3_6.png gave hash 513359294U not the expected 662622011U 159: file test3_7.png gave hash 98439579U not the expected 469729412U +212: ........[22:06:31] Explicit valence for atom # 1 O, 3, is greater than permitted 159: Done 159: ----------------- Test Github774: upside-down drawings 159: file test774_1.png gave hash 2947517748U not the expected 428322245U +183: [22:06:31] ------------------------------------- +183: [22:06:31] testing PatternHolder +212: .. +212: ---------------------------------------------------------------------- +212: Ran 38 tests in 9.823s +212: +212: OK +212: done 159: file test774_2.png gave hash 3968995771U not the expected 4095288521U 159: Done 159: ----------------- Test 9 (molecule legends) @@ -33484,7 +32508,327 @@ 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick 159: file test852_1.png gave hash 1401513420U not the expected 271517011U -152: .............[02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() +213/236 Test #212: pyMolStandardize ....................... Passed 10.31 sec +159: file test852_2.png gave hash 1268186246U not the expected 967452082U +159: ---------------- +159: ---------------- +159: ---------------- +159: ---------------- +159: Done +159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +159: file test860_1.png gave hash 2465667142U not the expected 2835587240U +159: file test860_2.png gave hash 3702727304U not the expected 1116015475U +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +214/236 Test #95: testEnumeration ........................ Passed 20.75 sec +159: file test860_3.png gave hash 524479710U not the expected 1872467868U +159: Done +159: ----------------- Test Github #910: ugly coordinates generated for peptide chains +183: [22:06:31] ------------------------------------- +183: [22:06:31] testing TautomerPatternHolder +159: Done +159: ----------------- Test Github #932: mistake in SVG for wedged bonds +159: Done +159: ----------------- Test Github #953: default color should not be cyan +159: Done +159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +159: Done +159: ----------------- Test Deuterium, Tritium +159: Done +159: ----------------- Test crossed bonds +159: Done +159: ----------------- Testing drawing a second molecule +159: Done +159: ----------------- Testing drawing a grid of molecules +159: Done +159: ----------------- Testing drawMolecules +183: [22:06:32] ------------------------------------- +183: [22:06:32] testSegFaultInHolder +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: [22:06:32] SMILES Parse Error: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1:[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1:[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] [22:06:32] [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: check for mistakes around position [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] 1: +183: SMILES Parse Error: [22:06:32] syntax error while parsing: dsafsdf +183: [22:06:32] [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +159: file test12_1.svg gave hash 76786371U not the expected 826649652U +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf for input: '[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf[22:06:32] dsafsdf +183: SMILES Parse Error: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: check for mistakes around position +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ' +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -33787,46 +33131,733 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -215/236 Test #177: pyCIPLabelsValidation .................. Passed 17.98 sec -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test852_2.png gave hash 1268186246U not the expected 967452082U -159: ---------------- -159: ---------------- -159: ---------------- -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: ---------------- -159: Done -159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test860_1.png gave hash 2465667142U not the expected 2835587240U -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test860_2.png gave hash 3702727304U not the expected 1116015475U -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test860_3.png gave hash 524479710U not the expected 1872467868U -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test Github #910: ugly coordinates generated for peptide chains -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test Github #932: mistake in SVG for wedged bonds -159: Done -159: ----------------- Test Github #953: default color should not be cyan -159: Done -159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Test Deuterium, Tritium -159: Done -159: ----------------- Test crossed bonds -159: Done -159: ----------------- Testing drawing a second molecule -152: [02:04:18] Molecule does not have explicit Hs. Consider calling AddHs() -159: Done -159: ----------------- Testing drawing a grid of molecules -159: Done -159: ----------------- Testing drawMolecules -159: file test12_1.svg gave hash 76786371U not the expected 826649652U +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +215/236 Test #177: pyCIPLabelsValidation .................. Passed 17.86 sec +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] [22:06:32] SMILES Parse Error: syntax error[22:06:32] SMILES Parse Error: syntax error while parsing: [22:06:32] [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: SMILES Parse Error: [22:06:32] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: syntax error[22:06:32] SMILES Parse Error: check for mistakes around position 1[22:06:32] dsafsdf +183: dsafsdf +183: while parsing: dsafsdf +183: [22:06:32] [22:06:32] [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] SMILES Parse Error: check for mistakes around position ^dsafsdf[22:06:32] : +183: [22:06:32] SMILES Parse Error: [22:06:32] dsafsdfSMILES Parse Error: +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdfsyntax error while parsing: +183: +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1:[22:06:32] [22:06:32] [22:06:32] ^SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] ^ +183: +183: +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: : +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [22:06:32] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] [22:06:32] dsafsdf +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILESdsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf[22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [22:06:32] SMILES Parse Error: check for mistakes around position 1: +183: [22:06:32] dsafsdf +183: [22:06:32] ^ +183: [22:06:32] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [22:06:32] ------------------------------------- +183: [22:06:32] Results do not depend on numThreads +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +216/236 Test #80: fileParsersCatchTest ................... Passed 21.81 sec 159: Done 159: ----------------- Test JSON Configuration 159: Done @@ -33871,27 +33902,30 @@ 159: file test20_4.png gave hash 284908271U not the expected 1714613205U 159: Done 159: ----------------- Test 21 - different font +152: .............[22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() 159: Done 159: ----------------- Test 22 - draw explicit methyls. +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:36] Molecule does not have explicit Hs. Consider calling AddHs() 159: Done 159: ----------------- Testing drawing of legends. 159: Done 159: ----------------- Test Github 3305 - change and scale line widths. -183: [02:04:19] ------------------------------------- -183: [02:04:19] Results do not depend on numThreads (all same) 159: file testGithub3305_1.png gave hash 3066881557U not the expected 3303791649U 159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U 159: file testGithub3305_3.png gave hash 748608900U not the expected 273338209U -183: [02:04:19] ------------------------------------- -183: [02:04:19] testTautomerQueries 159: file testGithub3305_4.png gave hash 3317652686U not the expected 3842605920U -183: [02:04:19] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [02:04:19] ------------------------------------- -183: [02:04:19] github3881 recursive smarts with rings 159: file testGithub3305_5.png gave hash 2008868897U not the expected 151279576U 159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U 159: file testGithub3305_6.png gave hash 1479310253U not the expected 613418460U -216/236 Test #183: substructLibraryTest ................... Passed 18.42 sec 159: file testGithub3305_7.png gave hash 526001191U not the expected 2835747678U 159: Done 159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. @@ -33904,186 +33938,8 @@ 159: Done 159: ----------------- Test AND queries 159: Done -217/236 Test #159: moldraw2DTest1 ......................... Passed 19.77 sec -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -218/236 Test #80: fileParsersCatchTest ................... Passed 21.68 sec -185: ......[02:04:20] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# 0x00007F5F6945D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 14# 0x00007F5F6B9CE62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 20# 0x00007F5F693B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F5F693B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F5F693B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F5F693B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F5F693B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 30# 0x00007F5F6B9CB3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# _PyObject_MakeTpCall in /usr/bin/python3 -185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 33# 0x00000000005C30D9 in /usr/bin/python3 -185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 35# 0x000000000064B89F in /usr/bin/python3 -185: 36# 0x000000000069ECA0 in /usr/bin/python3 -185: 37# _PyObject_MakeTpCall in /usr/bin/python3 -185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 39# 0x00000000005C30D9 in /usr/bin/python3 -185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 41# 0x000000000064B89F in /usr/bin/python3 -185: 42# 0x000000000069ECA0 in /usr/bin/python3 -185: 43# _PyObject_MakeTpCall in /usr/bin/python3 -185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 45# 0x00000000005C30D9 in /usr/bin/python3 -185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 47# 0x000000000064B89F in /usr/bin/python3 -185: 48# 0x000000000069ECA0 in /usr/bin/python3 -185: 49# _PyObject_MakeTpCall in /usr/bin/python3 -185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 51# 0x0000000000599C8E in /usr/bin/python3 -185: 52# _PyObject_MakeTpCall in /usr/bin/python3 -185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 54# PyEval_EvalCode in /usr/bin/python3 -185: 55# 0x000000000066DA21 in /usr/bin/python3 -185: 56# 0x0000000000669A8C in /usr/bin/python3 -185: 57# 0x0000000000682973 in /usr/bin/python3 -185: 58# 0x0000000000682273 in /usr/bin/python3 -185: 59# 0x00000000006820AE in /usr/bin/python3 -185: 60# Py_RunMain in /usr/bin/python3 -185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x00007F5F6C311CA8 in /lib/x86_64-linux-gnu/libc.so.6 -185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -185: 64# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -185: [02:04:20] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# 0x00007F5F68EE6800 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# 0x00007F5F6945D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# 0x00007F5F6B9CE62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F5F693B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F5F693B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F5F693B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F5F693B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x00007F5F693B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# 0x00007F5F6B9CB3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 32# _PyObject_MakeTpCall in /usr/bin/python3 -185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 34# 0x00000000005C30D9 in /usr/bin/python3 -185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 36# 0x000000000064B89F in /usr/bin/python3 -185: 37# 0x000000000069ECA0 in /usr/bin/python3 -185: 38# _PyObject_MakeTpCall in /usr/bin/python3 -185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 40# 0x00000000005C30D9 in /usr/bin/python3 -185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 42# 0x000000000064B89F in /usr/bin/python3 -185: 43# 0x000000000069ECA0 in /usr/bin/python3 -185: 44# _PyObject_MakeTpCall in /usr/bin/python3 -185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 46# 0x00000000005C30D9 in /usr/bin/python3 -185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 48# 0x000000000064B89F in /usr/bin/python3 -185: 49# 0x000000000069ECA0 in /usr/bin/python3 -185: 50# _PyObject_MakeTpCall in /usr/bin/python3 -185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 52# 0x0000000000599C8E in /usr/bin/python3 -185: 53# _PyObject_MakeTpCall in /usr/bin/python3 -185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 55# PyEval_EvalCode in /usr/bin/python3 -185: 56# 0x000000000066DA21 in /usr/bin/python3 -185: 57# 0x0000000000669A8C in /usr/bin/python3 -185: 58# 0x0000000000682973 in /usr/bin/python3 -185: 59# 0x0000000000682273 in /usr/bin/python3 -185: 60# 0x00000000006820AE in /usr/bin/python3 -185: 61# Py_RunMain in /usr/bin/python3 -185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x00007F5F6C311CA8 in /lib/x86_64-linux-gnu/libc.so.6 -185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -185: 65# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -219/236 Test #95: testEnumeration ........................ Passed 22.59 sec -152: ...[02:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: [02:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: ... -152: ---------------------------------------------------------------------- -152: Ran 19 tests in 21.104s -152: -152: OK -152: Testing MolAlign Wrappers -220/236 Test #152: pyMolAlign ............................. Passed 21.61 sec -195: ..[02:04:21] +217/236 Test #159: moldraw2DTest1 ......................... Passed 24.47 sec +195: ..[22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34097,7 +33953,7 @@ 195: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34108,17 +33964,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34150,13 +34006,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [02:04:21] +195: [22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34170,7 +34026,7 @@ 195: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34181,17 +34037,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34223,13 +34079,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [02:04:21] +195: [22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34243,7 +34099,7 @@ 195: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34254,17 +34110,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34296,13 +34152,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [02:04:21] +195: [22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34316,7 +34172,7 @@ 195: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34327,17 +34183,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34369,13 +34225,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [02:04:21] +195: [22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34389,7 +34245,7 @@ 195: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34400,17 +34256,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34442,13 +34298,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .....[02:04:21] +195: .....[22:06:38] 195: 195: **** 195: Range Error @@ -34462,7 +34318,7 @@ 195: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34473,17 +34329,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34515,49 +34371,49 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ......[02:04:21] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [02:04:21] ERROR: Smiles parse error on line 0 -195: [02:04:21] ERROR: Cannot create molecule from : 'c1ccccc' -195: [02:04:21] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [02:04:21] SMILES Parse Error: check for mistakes around position 2: -195: [02:04:21] C(C -195: [02:04:21] ~^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [02:04:21] ERROR: Smiles parse error on line 3 -195: [02:04:21] ERROR: Cannot create molecule from : 'C(C' -195: [02:04:21] Explicit valence for atom # 1 C, 5, is greater than permitted -195: [02:04:21] ERROR: Could not sanitize molecule on line 6 -195: [02:04:21] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -195: [02:04:21] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [02:04:21] ERROR: Smiles parse error on line 0 -195: [02:04:21] ERROR: Cannot create molecule from : 'c1ccccc' -195: [02:04:21] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [02:04:21] SMILES Parse Error: check for mistakes around position 2: -195: [02:04:21] C(C -195: [02:04:21] ~^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [02:04:21] ERROR: Smiles parse error on line 3 -195: [02:04:21] ERROR: Cannot create molecule from : 'C(C' -195: [02:04:21] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -195: [02:04:21] ERROR: Smiles parse error on line 6 -195: [02:04:21] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -195: [02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] ERROR: Could not sanitize molecule ending on line 21 -195: [02:04:21] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] ERROR: EOF hit while reading atoms -195: [02:04:21] ERROR: moving to the beginning of the next molecule -195: [02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] ERROR: Could not sanitize molecule ending on line 21 -195: [02:04:21] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] ERROR: EOF hit while reading atoms -195: [02:04:21] ERROR: moving to the beginning of the next molecule -195: ....[02:04:21] +195: ......[22:06:38] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [22:06:38] ERROR: Smiles parse error on line 0 +195: [22:06:38] ERROR: Cannot create molecule from : 'c1ccccc' +195: [22:06:38] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [22:06:38] SMILES Parse Error: check for mistakes around position 2: +195: [22:06:38] C(C +195: [22:06:38] ~^ +195: [22:06:38] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [22:06:38] ERROR: Smiles parse error on line 3 +195: [22:06:38] ERROR: Cannot create molecule from : 'C(C' +195: [22:06:38] Explicit valence for atom # 1 C, 5, is greater than permitted +195: [22:06:38] ERROR: Could not sanitize molecule on line 6 +195: [22:06:38] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +195: [22:06:38] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [22:06:38] ERROR: Smiles parse error on line 0 +195: [22:06:38] ERROR: Cannot create molecule from : 'c1ccccc' +195: [22:06:38] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [22:06:38] SMILES Parse Error: check for mistakes around position 2: +195: [22:06:38] C(C +195: [22:06:38] ~^ +195: [22:06:38] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [22:06:38] ERROR: Smiles parse error on line 3 +195: [22:06:38] ERROR: Cannot create molecule from : 'C(C' +195: [22:06:38] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +195: [22:06:38] ERROR: Smiles parse error on line 6 +195: [22:06:38] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +195: [22:06:38] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:38] ERROR: Could not sanitize molecule ending on line 21 +195: [22:06:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:38] ERROR: EOF hit while reading atoms +195: [22:06:38] ERROR: moving to the beginning of the next molecule +195: [22:06:38] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:38] ERROR: Could not sanitize molecule ending on line 21 +195: [22:06:38] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:38] ERROR: EOF hit while reading atoms +195: [22:06:38] ERROR: moving to the beginning of the next molecule +195: ....[22:06:38] 195: 195: **** 195: Pre-condition Violation @@ -34571,7 +34427,7 @@ 195: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34582,17 +34438,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34624,13 +34480,13 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .............[02:04:21] +195: .............[22:06:38] 195: 195: **** 195: Range Error @@ -34644,7 +34500,7 @@ 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x00007F8F27CEC62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x00007F8742A2062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34655,17 +34511,17 @@ 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x00007F8F253B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x00007F8F253B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x00007F8F253B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x00007F8F253B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x00007F8F253B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x00007F87401B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x00007F87401B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x00007F87401B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x00007F87401B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x00007F87401B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x00007F8F27CE93C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x00007F8742A1D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x00000000005C30D9 in /usr/bin/python3 @@ -34697,108 +34553,120 @@ 195: 55# 0x00000000006820AE in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x00007F8F284C6CA8 in /lib/x86_64-linux-gnu/libc.so.6 +195: 58# 0x00007F87431FACA8 in /lib/x86_64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ...[02:04:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: ............................[02:04:21] SMILES Parse Error: unclosed ring for input: 'C1CC' +195: ...[22:06:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: ............................[22:06:38] SMILES Parse Error: unclosed ring for input: 'C1CC' 195: ......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| 195: 643 -195: ..[02:04:21] WARNING: not removing hydrogen atom without neighbors -195: [02:04:21] WARNING: not removing hydrogen atom with dummy atom neighbors -195: [02:04:21] WARNING: not removing hydrogen atom with wedged bond -195: [02:04:21] WARNING: not removing hydrogen atom without neighbors -195: [02:04:21] WARNING: not removing hydrogen atom with dummy atom neighbors -195: ......[02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: .[02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [02:04:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [02:04:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [02:04:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: ..........[02:04:21] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [02:04:21] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: .[02:04:21] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [02:04:21] SMILES Parse Error: check for mistakes around position 4: -195: [02:04:21] CCC |$foo;;bar$| ourname -195: [02:04:21] ~~~^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: ..[02:04:21] SMILES Parse Error: syntax error while parsing: error -195: [02:04:21] SMILES Parse Error: check for mistakes around position 1: -195: [02:04:21] error -195: [02:04:21] ^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -195: [02:04:21] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -195: [02:04:21] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -195: .........................[02:04:21] SMILES Parse Error: syntax error while parsing: garbage_0 -195: [02:04:21] SMILES Parse Error: check for mistakes around position 1: -195: [02:04:21] garbage_0 -195: [02:04:21] ^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -195: [02:04:21] SMILES Parse Error: syntax error while parsing: garbage_2 -195: [02:04:21] SMILES Parse Error: check for mistakes around position 1: -195: [02:04:21] garbage_2 -195: [02:04:21] ^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -195: [02:04:21] SMILES Parse Error: syntax error while parsing: garbage_4 -195: [02:04:21] SMILES Parse Error: check for mistakes around position 1: -195: [02:04:21] garbage_4 -195: [02:04:21] ^ -195: [02:04:21] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +195: ..[22:06:38] WARNING: not removing hydrogen atom without neighbors +195: [22:06:38] WARNING: not removing hydrogen atom with dummy atom neighbors +195: [22:06:38] WARNING: not removing hydrogen atom with wedged bond +195: [22:06:38] WARNING: not removing hydrogen atom without neighbors +195: [22:06:38] WARNING: not removing hydrogen atom with dummy atom neighbors +195: ......[22:06:39] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: .[22:06:39] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:39] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:39] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:39] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [22:06:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [22:06:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [22:06:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: ..........[22:06:39] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [22:06:39] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: .[22:06:39] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [22:06:39] SMILES Parse Error: check for mistakes around position 4: +195: [22:06:39] CCC |$foo;;bar$| ourname +195: [22:06:39] ~~~^ +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: ..[22:06:39] SMILES Parse Error: syntax error while parsing: error +195: [22:06:39] SMILES Parse Error: check for mistakes around position 1: +195: [22:06:39] error +195: [22:06:39] ^ +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +195: [22:06:39] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +195: [22:06:39] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +183: [22:06:39] ------------------------------------- +183: [22:06:39] Results do not depend on numThreads (all same) +195: .........................[22:06:39] SMILES Parse Error: syntax error while parsing: garbage_0 +195: [22:06:39] SMILES Parse Error: check for mistakes around position 1: +195: [22:06:39] garbage_0 +195: [22:06:39] ^ +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +195: [22:06:39] SMILES Parse Error: syntax error while parsing: garbage_2 +195: [22:06:39] SMILES Parse Error: check for mistakes around position 1: +195: [22:06:39] garbage_2 +195: [22:06:39] ^ +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +195: [22:06:39] SMILES Parse Error: syntax error while parsing: garbage_4 +195: [22:06:39] SMILES Parse Error: check for mistakes around position 1: +195: [22:06:39] garbage_4 +195: [22:06:39] ^ +195: [22:06:39] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 195: ............ 195: ---------------------------------------------------------------------- -195: Ran 279 tests in 18.462s +195: Ran 279 tests in 18.774s 195: 195: OK 195: supplier: 195: supplier: 195: supplier: -221/236 Test #195: pyGraphMolWrap ......................... Passed 19.67 sec -173: [02:04:22] Complex queries can be slow. +183: [22:06:39] ------------------------------------- +183: [22:06:39] testTautomerQueries +183: [22:06:39] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [22:06:39] ------------------------------------- +183: [22:06:39] github3881 recursive smarts with rings +218/236 Test #183: substructLibraryTest ................... Passed 24.29 sec +152: ...[22:06:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [22:06:39] Molecule does not have explicit Hs. Consider calling AddHs() +219/236 Test #195: pyGraphMolWrap ......................... Passed 19.86 sec +152: ... +152: ---------------------------------------------------------------------- +152: Ran 19 tests in 25.868s +152: +152: OK +152: Testing MolAlign Wrappers +220/236 Test #152: pyMolAlign ............................. Passed 26.77 sec +221/236 Test #199: pyTestThreads .......................... Passed 19.47 sec 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -173: [02:04:23] Complex queries can be slow. -173: [02:04:23] Complex queries can be slow. 29: All 191 tests passed -173: [02:04:23] Complex queries can be slow. -173: [02:04:23] Complex queries can be slow. 29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -173: [02:04:23] Complex queries can be slow. -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 24.749s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -222/236 Test #185: pySubstructLibrary ..................... Passed 25.44 sec -173: [02:04:26] Complex queries can be slow. +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +173: [22:06:41] Complex queries can be slow. +173: [22:06:41] Complex queries can be slow. +173: [22:06:43] Complex queries can be slow. +173: [22:06:43] Complex queries can be slow. +173: [22:06:43] Complex queries can be slow. +173: [22:06:43] Complex queries can be slow. 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: TOTAL Time elapsed 26.81 seconds -173: [02:04:26] Complex queries can be slow. -223/236 Test #163: testFMCS ............................... Passed 26.94 sec -173: [02:04:26] Complex queries can be slow. -173: [02:04:27] Complex queries can be slow. -173: [02:04:27] Complex queries can be slow. -173: [02:04:27] Complex queries can be slow. -173: [02:04:27] Complex queries can be slow. -173: [02:04:28] Complex queries can be slow. -173: [02:04:28] Complex queries can be slow. -173: [02:04:28] Complex queries can be slow. +163: TOTAL Time elapsed 30.65 seconds +51: Randomness seeded to: 546823872 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: +222/236 Test #51: canonTestsCatch ........................ Passed 33.73 sec +223/236 Test #163: testFMCS ............................... Passed 30.77 sec +173: [22:06:44] Complex queries can be slow. +173: [22:06:44] Complex queries can be slow. +173: [22:06:44] Complex queries can be slow. +173: [22:06:44] Complex queries can be slow. +173: [22:06:44] Complex queries can be slow. +173: [22:06:45] Complex queries can be slow. +173: [22:06:45] Complex queries can be slow. 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -34806,44 +34674,235 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -173: [02:04:28] Complex queries can be slow. -173: [02:04:28] Complex queries can be slow. -51: Randomness seeded to: 1283534727 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -224/236 Test #51: canonTestsCatch ........................ Passed 31.04 sec +148: .........[22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [22:06:45] Molecule does not have explicit Hs. Consider calling AddHs() +173: [22:06:45] Complex queries can be slow. +173: [22:06:45] Complex queries can be slow. +185: ......[22:06:45] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x00007FD7E545D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x00007FD7E782762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x00007FD7E53B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007FD7E53B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FD7E53B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FD7E53B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FD7E53B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x00007FD7E78243C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# _PyObject_MakeTpCall in /usr/bin/python3 +185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 33# 0x00000000005C30D9 in /usr/bin/python3 +185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 35# 0x000000000064B89F in /usr/bin/python3 +185: 36# 0x000000000069ECA0 in /usr/bin/python3 +185: 37# _PyObject_MakeTpCall in /usr/bin/python3 +185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 39# 0x00000000005C30D9 in /usr/bin/python3 +185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 41# 0x000000000064B89F in /usr/bin/python3 +185: 42# 0x000000000069ECA0 in /usr/bin/python3 +185: 43# _PyObject_MakeTpCall in /usr/bin/python3 +185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 45# 0x00000000005C30D9 in /usr/bin/python3 +185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 47# 0x000000000064B89F in /usr/bin/python3 +185: 48# 0x000000000069ECA0 in /usr/bin/python3 +185: 49# _PyObject_MakeTpCall in /usr/bin/python3 +185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 51# 0x0000000000599C8E in /usr/bin/python3 +185: 52# _PyObject_MakeTpCall in /usr/bin/python3 +185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 54# PyEval_EvalCode in /usr/bin/python3 +185: 55# 0x000000000066DA21 in /usr/bin/python3 +185: 56# 0x0000000000669A8C in /usr/bin/python3 +185: 57# 0x0000000000682973 in /usr/bin/python3 +185: 58# 0x0000000000682273 in /usr/bin/python3 +185: 59# 0x00000000006820AE in /usr/bin/python3 +185: 60# Py_RunMain in /usr/bin/python3 +185: 61# Py_BytesMain in /usr/bin/python3 +185: 62# 0x00007FD7E816ACA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +185: 64# _start in /usr/bin/python3 +185: ---------- +185: **** +185: +185: [22:06:45] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x00007FD7E4EE6800 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x00007FD7E545D1D5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x00007FD7E782762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007FD7E53B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FD7E53B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FD7E53B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FD7E53B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x00007FD7E53B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 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-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x00007FD7E78243C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 32# _PyObject_MakeTpCall in /usr/bin/python3 +185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 34# 0x00000000005C30D9 in /usr/bin/python3 +185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 36# 0x000000000064B89F in /usr/bin/python3 +185: 37# 0x000000000069ECA0 in /usr/bin/python3 +185: 38# _PyObject_MakeTpCall in /usr/bin/python3 +185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 40# 0x00000000005C30D9 in /usr/bin/python3 +185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 42# 0x000000000064B89F in /usr/bin/python3 +185: 43# 0x000000000069ECA0 in /usr/bin/python3 +185: 44# _PyObject_MakeTpCall in /usr/bin/python3 +185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 46# 0x00000000005C30D9 in /usr/bin/python3 +185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 48# 0x000000000064B89F in /usr/bin/python3 +185: 49# 0x000000000069ECA0 in /usr/bin/python3 +185: 50# _PyObject_MakeTpCall in /usr/bin/python3 +185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 52# 0x0000000000599C8E in /usr/bin/python3 +185: 53# _PyObject_MakeTpCall in /usr/bin/python3 +185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 55# PyEval_EvalCode in /usr/bin/python3 +185: 56# 0x000000000066DA21 in /usr/bin/python3 +185: 57# 0x0000000000669A8C in /usr/bin/python3 +185: 58# 0x0000000000682973 in /usr/bin/python3 +185: 59# 0x0000000000682273 in /usr/bin/python3 +185: 60# 0x00000000006820AE in /usr/bin/python3 +185: 61# Py_RunMain in /usr/bin/python3 +185: 62# Py_BytesMain in /usr/bin/python3 +185: 63# 0x00007FD7E816ACA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +185: 65# _start in /usr/bin/python3 +185: ---------- +185: **** +185: 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -173: [02:04:29] Complex queries can be slow. +173: [22:06:45] Complex queries can be slow. +173: [22:06:46] Complex queries can be slow. +173: [22:06:46] Complex queries can be slow. +173: [22:06:46] Complex queries can be slow. 173: =============================================================================== 173: All tests passed (121 assertions in 17 test cases) 173: -225/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 28.93 sec -148: .........[02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -148: [02:04:30] Molecule does not have explicit Hs. Consider calling AddHs() +224/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 32.83 sec +210: [22:06:48] Explicit valence for atom # 0 Br, 1, is greater than permitted +210: =============================================================================== +210: All tests passed (38344 assertions in 51 test cases) +210: +225/236 Test #210: molStandardizeCatchTest ................ Passed 26.95 sec +148: ... +148: ---------------------------------------------------------------------- +148: Ran 22 tests in 34.674s +148: +148: OK +226/236 Test #148: pyDistGeomHelpers ...................... Passed 35.74 sec +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 29.693s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +227/236 Test #185: pySubstructLibrary ..................... Passed 33.01 sec +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +29: All 191 tests passed +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +228/236 Test #150: testO3AAlign ........................... Passed 41.15 sec +147: [22:06:56] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [22:06:56] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [22:06:56] UFFTYPER: Unrecognized charge state for atom: 0 +5: [22:06:57] Finished: testMultipleTimes() +5: [22:06:57] +5: ----------------------------------------- +229/236 Test #5: testConcurrentQueue .................... Passed 46.92 sec 29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 29: All 191 tests passed 29: done @@ -34860,64 +34919,27 @@ 29: ------------------------------------- 29: Unit test for MMFF butane scan. 29: done -226/236 Test #29: testMMFFForceField ..................... Passed 33.80 sec -210: [02:04:32] Explicit valence for atom # 0 Br, 1, is greater than permitted -210: =============================================================================== -210: All tests passed (38344 assertions in 51 test cases) -210: -227/236 Test #210: molStandardizeCatchTest ................ Passed 27.98 sec -148: ... -148: ---------------------------------------------------------------------- -148: Ran 22 tests in 36.411s -148: -148: OK -228/236 Test #148: pyDistGeomHelpers ...................... Passed 37.08 sec -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -229/236 Test #150: testO3AAlign ........................... Passed 45.42 sec -147: [02:04:55] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [02:04:55] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [02:04:55] UFFTYPER: Unrecognized charge state for atom: 0 -236: DbCLI/UnitTestDbCLI.py ............ [100%] -236: -236: =============================== warnings summary =============================== -236: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 -236: /build/reproducible-path/rdkit-202503.1/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) -236: decBase = declarative_base() -236: -236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 57.22s ======================== -230/236 Test #236: pythonProjectTests ..................... Passed 58.15 sec -146: [02:05:16] done -5: [02:05:18] Finished: testMultipleTimes() -5: [02:05:18] -5: ----------------------------------------- -231/236 Test #5: testConcurrentQueue .................... Passed 82.82 sec -146: [02:05:16] --------------------------------- -146: [02:05:16] test github issue 256: handling of zero-atom molecules +230/236 Test #29: testMMFFForceField ..................... Passed 47.92 sec +146: [22:07:15] done +146: [22:07:15] --------------------------------- +146: [22:07:15] test github issue 256: handling of zero-atom molecules 146: -146: [02:05:16] --------------------------------- -146: [02:05:16] test embedder callback function -146: [02:05:16] --------------------------------- -146: [02:05:16] test multi-threaded multi-conf embedding +146: [22:07:15] --------------------------------- +146: [22:07:15] test embedder callback function +146: [22:07:15] --------------------------------- +146: [22:07:15] test multi-threaded multi-conf embedding 146: -146: [02:05:19] --------------------------------- -146: [02:05:19] test github issue 563: Incorrect ring stereochemistry after embedding +146: [22:07:21] --------------------------------- +146: [22:07:21] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [02:05:20] --------------------------------- -146: [02:05:20] test github issue 568: Incorrect stereochemistry after embedding +146: [22:07:23] --------------------------------- +146: [22:07:23] test github issue 568: Incorrect stereochemistry after embedding 146: 146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -232/236 Test #171: testRascalCluster ...................... Passed 84.05 sec 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O @@ -34926,19 +34948,20 @@ 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +170: =============================================================================== +170: All tests passed (3590 assertions in 35 test cases) +170: +231/236 Test #170: testRascalMCES ......................... Passed 78.66 sec 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +232/236 Test #171: testRascalCluster ...................... Passed 79.46 sec 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -170: =============================================================================== -170: All tests passed (3590 assertions in 35 test cases) -170: -233/236 Test #170: testRascalMCES ......................... Passed 91.30 sec -146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 -146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 -147: [02:05:33] Interrupted, cancelling conformer generation +147: [22:07:35] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] @@ -34971,11 +34994,14 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 -146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -234/236 Test #147: distGeomHelpersCatch ................... Passed 94.40 sec +233/236 Test #147: distGeomHelpersCatch ................... Passed 83.01 sec +146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 @@ -34983,48 +35009,58 @@ 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -146: [02:05:52] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:05:43] --------------------------------- -146: [02:05:43] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [02:05:43] --------------------------------- -146: [02:05:43] More ChEMBL molecules failing bounds smoothing. -146: [02:05:43] --------------------------------- -146: [02:05:43] ugly conformations can be generated for highly constrained ring systems. -146: [02:05:43] --------------------------------- -146: [02:05:43] test embed parameters structure. -146: [02:05:43] --------------------------------- -146: [02:05:43] test github 1227: Hs being used in RMSD filtering. -146: [02:05:43] --------------------------------- -146: [02:05:43] Failure to embed larger aromatic rings. -146: [02:05:44] --------------------------------- -146: [02:05:44] Deterministic with large random seeds -146: [02:05:47] --------------------------------- -146: [02:05:47] Github #1990: seg fault after RemoveHs -146: [02:05:47] --------------------------------- -146: [02:05:47] Github #2246: Use coordMap when starting embedding from random coords -146: [02:05:51] --------------------------------- -146: [02:05:51] Providing a distance bounds matrix. -146: [02:05:51] --------------------------------- -146: [02:05:51] Disabling fragmentation. -146: [02:05:51] --------------------------------- -146: [02:05:51] Using symmetry in conformation pruning. -146: [02:05:52] --------------------------------- -146: [02:05:52] Force trans amides. -146: [02:05:52] --------------------------------- -146: [02:05:52] test missing Hs warning. -146: [02:05:52] --------------------------------- -146: [02:05:52] basic H bond support. -146: [02:05:52] ******************************************************* -235/236 Test #146: testDistGeomHelpers .................... Passed 113.02 sec -174: Randomness seeded to: 2021204065 +146: [22:07:47] Molecule does not have explicit Hs. Consider calling AddHs() +146: [22:07:41] --------------------------------- +146: [22:07:41] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [22:07:41] --------------------------------- +146: [22:07:41] More ChEMBL molecules failing bounds smoothing. +146: [22:07:41] --------------------------------- +146: [22:07:41] ugly conformations can be generated for highly constrained ring systems. +146: [22:07:41] --------------------------------- +146: [22:07:41] test embed parameters structure. +146: [22:07:41] --------------------------------- +146: [22:07:41] test github 1227: Hs being used in RMSD filtering. +146: [22:07:41] --------------------------------- +146: [22:07:41] Failure to embed larger aromatic rings. +146: [22:07:43] --------------------------------- +146: [22:07:43] Deterministic with large random seeds +146: [22:07:45] --------------------------------- +146: [22:07:45] Github #1990: seg fault after RemoveHs +146: [22:07:45] --------------------------------- +146: [22:07:45] Github #2246: Use coordMap when starting embedding from random coords +146: [22:07:47] --------------------------------- +146: [22:07:47] Providing a distance bounds matrix. +146: [22:07:47] --------------------------------- +146: [22:07:47] Disabling fragmentation. +146: [22:07:47] --------------------------------- +146: [22:07:47] Using symmetry in conformation pruning. +146: [22:07:47] --------------------------------- +146: [22:07:47] Force trans amides. +146: [22:07:47] --------------------------------- +146: [22:07:47] test missing Hs warning. +146: [22:07:47] --------------------------------- +146: [22:07:47] basic H bond support. +146: [22:07:47] ******************************************************* +234/236 Test #146: testDistGeomHelpers .................... Passed 95.26 sec +174: Randomness seeded to: 483364153 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 167.24 sec +235/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 108.51 sec +236: DbCLI/UnitTestDbCLI.py ............ [100%] +236: +236: =============================== warnings summary =============================== +236: ../obj-x86_64-linux-gnu/rdkit/Chem/MolDb/Loader_sa.py:20 +236: /build/reproducible-path/rdkit-202503.1/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) +236: decBase = declarative_base() +236: +236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html +236: ================== 12 passed, 1 warning in 115.30s (0:01:55) =================== +236/236 Test #236: pythonProjectTests ..................... Passed 117.26 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 172.18 sec +Total Test time (real) = 129.88 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp @@ -35034,7 +35070,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -35045,1278 +35081,1278 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Randomize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MACCSkeys.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey --- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbInfo.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbConnection.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbResultSet.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/MolKey.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/Enumerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FilterCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MACCSkeys.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PropertyMol.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors3D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/FreeSans.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/IPythonConsole.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/FraggleSim.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/RegistrationHash.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ReducedGraphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Sheridan.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/conftest.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png -- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png --- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb --- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg --- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/conf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/style.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdkit_fork_clone.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/style.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_40_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdkit_fork_clone.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2025.03.1 @@ -36362,12 +36398,12 @@ -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/BetterEnums.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/enum.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -36988,7 +37024,10 @@ dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-313-x86_64-linux-gnu.so @@ -37033,14 +37072,11 @@ I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' @@ -37667,22 +37703,22 @@ dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake +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: 24 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 -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol byteain: 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_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 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 @@ -37697,15 +37733,15 @@ dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-2_all.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-2_all.deb'. +dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-2_amd64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-2_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-2_amd64.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-2_amd64.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-2_amd64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-2_amd64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-2_amd64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-2_all.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-2_amd64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-2_all.deb'. +dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-2_amd64.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37713,12 +37749,14 @@ 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/884034/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/884034/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/2321824 and its subdirectories -I: Current time: Sat May 16 02:13:46 -12 2026 -I: pbuilder-time-stamp: 1778940826 +I: removing directory /srv/workspace/pbuilder/884034 and its subdirectories +I: Current time: Sun Apr 13 22:15:11 +14 2025 +I: pbuilder-time-stamp: 1744532111